| Title: | Structural Exploration of the Gene Ontology (GO) Knowledge Base |
|---|---|
| Description: | It provides an effective, efficient, and fast way to explore the Gene Ontology (GO). Given a set of genes, the package contains functions to assess the GO and obtain the terms associated with the genes and the levels of the GO terms. The package provides functions for the three different GO ontology. We discussed the methods explicitly in the following article <doi:10.1038/s41598-020-73326-3>. |
| Authors: | Kalifa Manjang, Frank Emmert-Streib, Shailesh Tripathi, Olli Yli-Harja, Matthias Dehmer |
| Maintainer: | Kalifa Manjang <[email protected]> |
| License: | GPL-2 |
| Version: | 1.2.7 |
| Built: | 2025-02-26 05:49:10 UTC |
| Source: | https://github.com/cran/GOxploreR |
For a directed graph, the in-degree nodes are the nodes which have edges coming into them and the out-degree nodes are those which have edges going out of them. The degreeDistBP function shows the distribution of these degrees over a particular GO-level. A bar plot is obtain which shows how many nodes in the GO-level have a certain degree k.
degreeDistBP(level)degreeDistBP(level)
level |
A numeric value for the GO-level |
A plot showing the degree distribution
# Degree distribution of GO-terms on level 3 degreeDistBP(level = 3) # Degree distribution of GO-terms on level 9 degreeDistBP(level = 9)# Degree distribution of GO-terms on level 3 degreeDistBP(level = 3) # Degree distribution of GO-terms on level 9 degreeDistBP(level = 9)
For a directed graph, the in-degree nodes are the nodes which have edges coming into them and the out-degree nodes are those which have edges going out of them. The degreeDistCC function shows the distribution of these degrees over a particular GO level. A bar plot is obtain which shows how many nodes in the GO level have a certain degree k.
degreeDistCC(level)degreeDistCC(level)
level |
A numeric value for the GO level |
A plot showing the degree distribution
# Degree distribution of GO terms on level 8 degreeDistCC(level = 8) # Degree distribution of GO terms on level 6 degreeDistCC(level = 6)# Degree distribution of GO terms on level 8 degreeDistCC(level = 8) # Degree distribution of GO terms on level 6 degreeDistCC(level = 6)
For a directed graph, the in-degree nodes are the nodes which have edges coming into them and the out-degree nodes are those which have edges going out of them. The degreeDistMF function shows the distribution of these degrees over a particular GO-level. A bar plot is obtain which shows how many nodes in the GO-level have a certain degree k.
degreeDistMF(level)degreeDistMF(level)
level |
A numeric value for the GO-level |
A plot showing the degree distribution
# Degree distribution of GO-terms on level 3 degreeDistMF(level = 3) # Degree distribution of GO-terms on level 10 degreeDistMF(level = 10)# Degree distribution of GO-terms on level 3 degreeDistMF(level = 3) # Degree distribution of GO-terms on level 10 degreeDistMF(level = 10)
distRankingGO returns the ranking of GO-terms based on the GO-terms hierarchy level and the maximal depth of paths in the GO-DAG passing through these GO-terms.
distRankingGO(goterm, domain = "BP", plot = TRUE)distRankingGO(goterm, domain = "BP", plot = TRUE)
goterm |
A list of GO-terms to be ordered |
domain |
The ontology of the GO-terms. The default is "BP" |
plot |
If FALSE the visualisation of the ordering is not provided. The default is TRUE. |
The function returns the ordered GO-terms, the indices corresponding to these GO-terms, the distance between the GO-terms hierarchy level and the maximal depth of paths in the GO-DAG passing through these GO-terms and a plot of the visualisaiton by default.
goterm <- c("GO:0000278","GO:0006414","GO:0022403","GO:0006415", "GO:0045047","GO:0072599","GO:0006613","GO:0000184","GO:0070972", "GO:0006413","GO:0000087","GO:0000280","GO:0000279","GO:0006612", "GO:0000956","GO:0048285","GO:0019080","GO:0019083","GO:0043624", "GO:0006402","GO:0032984","GO:0006401","GO:0072594","GO:0019058", "GO:0051301","GO:0016071","GO:0006412","GO:0002682","GO:0022411", "GO:0006614") #The GO-terms in the list are ordered distRankingGO(goterm = goterm, domain = "BP", plot = TRUE)goterm <- c("GO:0000278","GO:0006414","GO:0022403","GO:0006415", "GO:0045047","GO:0072599","GO:0006613","GO:0000184","GO:0070972", "GO:0006413","GO:0000087","GO:0000280","GO:0000279","GO:0006612", "GO:0000956","GO:0048285","GO:0019080","GO:0019083","GO:0043624", "GO:0006402","GO:0032984","GO:0006401","GO:0072594","GO:0019058", "GO:0051301","GO:0016071","GO:0006412","GO:0002682","GO:0022411", "GO:0006614") #The GO-terms in the list are ordered distRankingGO(goterm = goterm, domain = "BP", plot = TRUE)
Retrieves the gene association GO-terms, also, the ontology of the terms as well as the respective levels based on the directed acyclic graph (DAG) are returned. The supported organisms are "Homo sapiens / Human", "Rattus norvegicus / Rat", "Mus musculus / Mouse", "Danio rerio / Zebrafish", "Caenorhabditis elegans / Worm", "Arabidopsis thaliana / cress", "Saccharomyces cerevisiae / Yeast", "Schizosaccharomyces pombe / Fission yeast", "Drosophila melanogaster / Fruit fly", "Escherichia coli / E.coli".
Gene2GOTermAndLevel(genes, organism, domain = NULL)Gene2GOTermAndLevel(genes, organism, domain = NULL)
genes |
A character vector of entrezgene id's belonging to an organism of interest |
organism |
An object of class character. A character string that defines the scientific / common name of the organism eg. Homo sapiens, Mouse. |
domain |
An optional object of class character. GO-terms have three domains .i.e. biological process (BP), molecular function (MF) and cellular component (CC). This character string identifies which of the three GO categories associated with the genes to return. GO-terms from one domain can be returned at a time. If NULL the biological process GO-terms will be obtained (default). |
A data.frame object that contains the genes, GO terms, ontology and GO-levels
This function is similar to Gene2GOTermAndLevel_ON, the difference is that the function do not query the
Ensembl database for GO terms (It is relatively faster) which means the results from Gene2GOTermAndLevel_ON function is always up to date.
# human genes v <- c(6713,4605,55143,10615,10212,4001,2146,11130,983,4085,9833,9134) # No value for domain is given so the default ("BP") is used Gene2GOTermAndLevel(genes = v, organism = "Homo sapiens") # The scientific names of the species can also be used Gene2GOTermAndLevel(genes = v, organism = "Homo sapiens", domain = "CC") Gene2GOTermAndLevel(genes = v, organism = "Human", domain = "MF")# human genes v <- c(6713,4605,55143,10615,10212,4001,2146,11130,983,4085,9833,9134) # No value for domain is given so the default ("BP") is used Gene2GOTermAndLevel(genes = v, organism = "Homo sapiens") # The scientific names of the species can also be used Gene2GOTermAndLevel(genes = v, organism = "Homo sapiens", domain = "CC") Gene2GOTermAndLevel(genes = v, organism = "Human", domain = "MF")
Retrieves the gene association GO-terms, also, the ontology of the terms as well as the respective levels based on the directed acyclic graph (DAG) are returned. A fast internet connection is needed for this funciton execution. The supported organisms are "Homo sapiens / Human", "Rattus norvegicus / Rat", "Mus musculus / Mouse", "Danio rerio / Zebrafish", "Caenorhabditis elegans / Worm" ,"Arabidopsis thaliana / Cress", "Saccharomyces cerevisiae / Yeast", "Schizosaccharomyces pombe / Fission yeast", "Drosophila melanogaster / Fruit fly".
Gene2GOTermAndLevel_ON(genes, organism, domain = NULL)Gene2GOTermAndLevel_ON(genes, organism, domain = NULL)
genes |
A character vector of entrezgene id's belonging to an organism of interest |
organism |
An object of class character. A character string that defines the scientific / common name of the organism eg. Homo sapiens, Mouse. |
domain |
An optional object of class character. GO-terms have three domains .i.e. biological process (BP), molecular function (MF) and cellular component (CC). This character string identifies which of the three GO categories associated with the genes to return. GO terms from one domain can be returned at a time. If NULL the biological process GO-terms will be obtained (default) |
A data.frame object that contains the genes, GO-terms, ontology and GO-levels
This function does not provide support for Escherichia coli.
# human genes v <- c(6713,4605, 10212, 9833, 6713) # No value for domain is given so the default ("BP") is used Gene2GOTermAndLevel_ON(genes = v, organism = "Human") # The scientific names of the species can also be used Gene2GOTermAndLevel_ON(genes = v, organism = "Homo sapiens", domain = "CC") Gene2GOTermAndLevel_ON(genes = v, organism = "Human", domain = "MF")# human genes v <- c(6713,4605, 10212, 9833, 6713) # No value for domain is given so the default ("BP") is used Gene2GOTermAndLevel_ON(genes = v, organism = "Human") # The scientific names of the species can also be used Gene2GOTermAndLevel_ON(genes = v, organism = "Homo sapiens", domain = "CC") Gene2GOTermAndLevel_ON(genes = v, organism = "Human", domain = "MF")
Derive the organism gene association GO-terms as an edgelist. It indicates how the terms are linked together. The supported organisms are "Homo sapiens / Human", "Rattus norvegicus / Rat", "Mus musculus / Mouse", "Danio rerio / Zebrafish","Caenorhabditis elegans / Worm" ,"Arabidopsis thaliana / Cress", "Saccharomyces cerevisiae / Yeast", "Schizosaccharomyces pombe / Fission yeast", "Drosophila melanogaster / Fruit fly", " Escherichia coli / E.coli"
GetDAG(organism, domain = "BP")GetDAG(organism, domain = "BP")
organism |
An object of class character that represents the organism. If the organism option is "BP", "MF" or "CC" the biological process, molecular function and cellular component general GO edgelist are obtained respectively |
domain |
The ontology of the GO-terms. The default is BP. |
A two-column matrix of the nodes and the edges to which they are connected
# Edgelist for entire GO BP ontology GetDAG(organism = "BP") # Edgelist for cellular component gene association GO-terms for organism Yeast GetDAG(organism = "Yeast", domain = "CC") # Edgelist for molecular function gene association GO-terms for organism Zebrafish GetDAG(organism = "Zebrafish", domain = "MF")# Edgelist for entire GO BP ontology GetDAG(organism = "BP") # Edgelist for cellular component gene association GO-terms for organism Yeast GetDAG(organism = "Yeast", domain = "CC") # Edgelist for molecular function gene association GO-terms for organism Zebrafish GetDAG(organism = "Zebrafish", domain = "MF")
Get the category of a GO-term. It checks if a GO-term is a jump node (RN), regular node (RN) or leaf node (LN).
getGOcategory(goterm)getGOcategory(goterm)
goterm |
An object with a category |
A data.frame object containing the terms, category and ontology.
goterm <- c("GO:0106003","GO:0032991","GO:1990429","GO:0002133","GO:0089713", "GO:1990666","GO:0036125") getGOcategory(goterm)goterm <- c("GO:0106003","GO:0032991","GO:1990429","GO:0002133","GO:0089713", "GO:1990666","GO:0036125") getGOcategory(goterm)
Returns all the leaf nodes from a particular organism-specific GO-DAG. If empty (or if "BP"), all the general BP GO-DAG leaf nodes will be returned. The supported organism are "Homo sapiens / Human", "Rattus norvegicus / Rat", "Mus musculus / Mouse", "Danio rerio / Zebrafish", "Caenorhabditis elegans / Worm" ,"Arabidopsis thaliana / Cress", "Saccharomyces cerevisiae / Yeast", "Schizosaccharomyces pombe / Fission yeast", "Drosophila melanogaster / Fruit fly", "Escherichia coli / E.coli".
GetLeafNodesBP(organism = NULL)GetLeafNodesBP(organism = NULL)
organism |
An object of class character that represents an organism |
A two-coloum matrix of all the leaf nodes in the organism-specific DAG and their respective levels
# General GO BP leaf nodes GetLeafNodesBP("BP") # Human BP GO-DAG leaf nodes GetLeafNodesBP(organism = "Human") # Mouse BP GO-DAG leaf nodes GetLeafNodesBP(organism = "DANIO RERIO")# General GO BP leaf nodes GetLeafNodesBP("BP") # Human BP GO-DAG leaf nodes GetLeafNodesBP(organism = "Human") # Mouse BP GO-DAG leaf nodes GetLeafNodesBP(organism = "DANIO RERIO")
Returns all the leaf nodes from a particular organism-specific GO-DAG. If empty (or if "CC"), all the general CC GO-DAG leaf nodes are returned. The supported organism are "Homo sapiens / Human", "Rattus norvegicus / Rat", "Mus musculus / Mouse", "Danio rerio / Zebrafish", "Caenorhabditis elegans / Worm", "Arabidopsis thaliana / Cress", "Saccharomyces cerevisiae / Yeast", "Schizosaccharomyces pombe / Fission yeast", "Drosophila melanogaster / Fruit fly", "Escherichia coli / E.coli".
GetLeafNodesCC(organism = NULL)GetLeafNodesCC(organism = NULL)
organism |
An object of class character that represents an organism |
A two-coloum matrix of all leaf nodes in the organism-specific DAG and their respective levels
# Zebrafish CC GO-DAG leaf nodes GetLeafNodesCC("Danio rerio") # Mouse CC GO-DAG leaf nodes GetLeafNodesCC("Zebrafish")# Zebrafish CC GO-DAG leaf nodes GetLeafNodesCC("Danio rerio") # Mouse CC GO-DAG leaf nodes GetLeafNodesCC("Zebrafish")
Returns all the leaf nodes from a particular organism-specific GO-DAG. If empty (or if "MF"), all the general MF GO-DAG leaf nodes are returned. The supported organisms are "Homo sapiens / Human", "Rattus norvegicus / Rat", "Mus musculus / Mouse", "Danio rerio / Zebrafish", "Caenorhabditis elegans / Worm", "Arabidopsis thaliana / Cress", "Saccharomyces cerevisiae / Yeast", "Schizosaccharomyces pombe / Fission yeast", "Drosophila melanogaster / Fruit fly", "Escherichia coli / E.coli".
GetLeafNodesMF(organism = NULL)GetLeafNodesMF(organism = NULL)
organism |
An object of class character that represents an organism. |
A two-coloum matrix of all the leaf nodes in the organism-specific DAG and their respective levels
# Mouse MF GO-DAG leaf nodes GetLeafNodesMF(organism = "Human") # Arabidopsis thaliana MF GO-DAG leaf nodes GetLeafNodesMF(organism = "Arabidopsis thaliana") # Drosophila melanogaster MF GO-DAG leaf nodes GetLeafNodesMF(organism = "Drosophila melanogaster")# Mouse MF GO-DAG leaf nodes GetLeafNodesMF(organism = "Human") # Arabidopsis thaliana MF GO-DAG leaf nodes GetLeafNodesMF(organism = "Arabidopsis thaliana") # Drosophila melanogaster MF GO-DAG leaf nodes GetLeafNodesMF(organism = "Drosophila melanogaster")
The GO2DecBP function provides a simple way to represent the biological process (BP) GO term. The function returns the descendant child nodes of a GO-term. In other words we begin from an ancestor term and find it's descendant child terms.
GO2DecBP(goterm)GO2DecBP(goterm)
goterm |
A string object of BP GO-term |
A vector comprising of GO-terms and the nodes they are linked to
v <- "GO:0000070" # BP GO term GO2DecBP(v) x <- "GO:0006725" GO2DecBP(x)v <- "GO:0000070" # BP GO term GO2DecBP(v) x <- "GO:0006725" GO2DecBP(x)
The GO2DecCC function provides a simple way to represent the cellular component (CC) GO-terms. The function returns the descendant child nodes of a GO-term. In other words we begin from an ancestor term and find it's descendant child terms.
GO2DecCC(goterm)GO2DecCC(goterm)
goterm |
A string object of CC GO-terms |
A vector comprising of GO-terms and the nodes they are linked to
v <- "GO:0000799" # CC GO term GO2DecCC(v) x <- "GO:0043231" GO2DecCC(x)v <- "GO:0000799" # CC GO term GO2DecCC(v) x <- "GO:0043231" GO2DecCC(x)
The GO2DecMF function provides a simple way to represent the molecular function (MF) GO-terms. TThe function returns the descedant child nodes of a GO term. In other words we begin from an ancestor term and find it's descendant child terms.
GO2DecMF(goterm)GO2DecMF(goterm)
goterm |
A string object of MF GO-terms |
A vector comprising of GO-terms and the nodes they are linked to
v <- "GO:0001228" # MF GO term GO2DecMF(v) x <- "GO:0005515" GO2DecMF(x)v <- "GO:0001228" # MF GO term GO2DecMF(v) x <- "GO:0005515" GO2DecMF(x)
The function contains all the GO-terms associated with the genes of an organism and their levels. If "BP", "MF" or "CC" the GO-terms from the whole ontology is return and their levels. The supported organisms are "Homo sapiens / Human", "Rattus norvegicus / Rat", "Mus musculus / Mouse", "Danio rerio / Zebrafish", "Caenorhabditis elegans / Worm" ,"Arabidopsis thaliana / Cress", "Saccharomyces cerevisiae / Yeast", "Schizosaccharomyces pombe / Fission yeast", "Drosophila melanogaster / Fruit fly", "Escherichia coli / E.coli".
GO4Organism(organism, domain = "BP")GO4Organism(organism, domain = "BP")
organism |
The organism supported by the package. Both the scientific / common name of the organism can be use |
domain |
The ontology of the GO-terms. The default is BP. |
A two-column matrix that contains the GO-terms and their GO-levels
# Return all the BP GO-terms associated with organism Homo sapiens GO4Organism(organism = "Homo sapiens") # Return all the CC GO-terms associated with organism Rat GO4Organism(organism = "Rat", domain = "CC")# Return all the BP GO-terms associated with organism Homo sapiens GO4Organism(organism = "Homo sapiens") # Return all the CC GO-terms associated with organism Rat GO4Organism(organism = "Rat", domain = "CC")
This function retrieves a GO BP term children's level i.e. for a GO-term it's children level are derived.
GOTermBP2ChildLevel(goterm)GOTermBP2ChildLevel(goterm)
goterm |
A character string of a valid gene ontology id e.g "GO:0097278" |
A list of children terms and their respective levels
# Retrieve "GO:0097278" children's level GOTermBP2ChildLevel(goterm = "GO:0097278") # Retrieve "GO:0051775" children's level GOTermBP2ChildLevel(goterm = "GO:0051775")# Retrieve "GO:0097278" children's level GOTermBP2ChildLevel(goterm = "GO:0097278") # Retrieve "GO:0051775" children's level GOTermBP2ChildLevel(goterm = "GO:0051775")
Gets the level of a GO biological process (BP) term based on the directed acyclic graph (DAG).
GOTermBPOnLevel(goterm)GOTermBPOnLevel(goterm)
goterm |
An object of class character. A character string of GO biological process (BP) term id. The object can be a GO-term or a vector of GO-terms |
A two-column matrix of the GO-terms and the level they map to
The Gene Ontology (GO) biological process (BP) tree was built using the root node "GO:0001850"
# A vector of biological process GO terms goterms <- c("GO:0006805","GO:0009083","GO:0006631") GOTermBPOnLevel(goterms) GOTermBPOnLevel("GO:0006629")# A vector of biological process GO terms goterms <- c("GO:0006805","GO:0009083","GO:0006631") GOTermBPOnLevel(goterms) GOTermBPOnLevel("GO:0006629")
This function retrieves a GO CC term children's level i.e. for a GO-term it's children level are derived.
GOTermCC2ChildLevel(goterm)GOTermCC2ChildLevel(goterm)
goterm |
A character string of a valid gene ontology id e.g "GO:0005737" |
A list of children terms and their respective levels
# Retrieve "GO:0005737" children's level GOTermCC2ChildLevel("GO:0005737") # Retrieve "GO:0099568" children's level GOTermCC2ChildLevel("GO:0099568")# Retrieve "GO:0005737" children's level GOTermCC2ChildLevel("GO:0005737") # Retrieve "GO:0099568" children's level GOTermCC2ChildLevel("GO:0099568")
Get the level of a GO cellular component (CC) term based on the directed acyclic graph (DAG)
GOTermCCOnLevel(goterm)GOTermCCOnLevel(goterm)
goterm |
An object of class character. A character string of GO cellular component (CC) terms. The object can be a GO-term or a vector of GO-terms |
A two-column matrix of the GO-terms and the level they map to
The Gene Ontology (GO) cellular component (CC) tree was built using the root node "GO:0005575"
# Cellular component GO terms goterms <- c("GO:0005634", "GO:0005737", "GO:0016020", "GO:0005743", "GO:0005739", "GO:0005759", "GO:0005829") GOTermCCOnLevel(goterms) GOTermCCOnLevel("GO:0005730")# Cellular component GO terms goterms <- c("GO:0005634", "GO:0005737", "GO:0016020", "GO:0005743", "GO:0005739", "GO:0005759", "GO:0005829") GOTermCCOnLevel(goterms) GOTermCCOnLevel("GO:0005730")
This function retrieves a GO MF term children's level i.e. for a GO-term it's children level are derived.
GOTermMF2ChildLevel(goterm)GOTermMF2ChildLevel(goterm)
goterm |
A character string of a valid gene ontology id e.g "GO:0004518" |
A list of children terms and their respective levels
# Retrieve "GO:0000978" children's level GOTermMF2ChildLevel(goterm = "GO:0000978") # Retrieve "GO:0004518" children's level GOTermMF2ChildLevel(goterm = "GO:0004518")# Retrieve "GO:0000978" children's level GOTermMF2ChildLevel(goterm = "GO:0000978") # Retrieve "GO:0004518" children's level GOTermMF2ChildLevel(goterm = "GO:0004518")
Gets the level of a molecular function (MF) term based on the directed acyclic graph (DAG) defined by the Gene Ontology consortium
GOTermMFOnLevel(goterm)GOTermMFOnLevel(goterm)
goterm |
An object of class character. A character string of GO molecular function (MF) terms. The object can be a GO-term or a vector of GO-terms |
A two-column matrix of the GO-terms and the level they map to
The Gene Ontology (GO) molecular function (MF) tree was built using the root node "GO:0003674"
# molecular function GO terms goterms <- c("GO:0003674","GO:0005515","GO:0003712","GO:0002039","GO:0000978","GO:0016740") GOTermMFOnLevel(goterms) GOTermMFOnLevel("GO:0005542")# molecular function GO terms goterms <- c("GO:0003674","GO:0005515","GO:0003712","GO:0002039","GO:0000978","GO:0016740") GOTermMFOnLevel(goterms) GOTermMFOnLevel("GO:0005542")
Gets all the biological process (BP) GO-terms on a GO-level. The supported organisms are "Homo sapiens / Human", "Rattus norvegicus / Rat", "Mus musculus / Mouse", "Danio rerio / Zebrafish", "Caenorhabditis elegans / Worm" ,"Arabidopsis thaliana / Cress", "Saccharomyces cerevisiae / Yeast", "Schizosaccharomyces pombe / Fission yeast", "Drosophila melanogaster / Fruit fly", "Escherichia coli / E.coli".
Level2GOTermBP(level, organism = NULL)Level2GOTermBP(level, organism = NULL)
level |
A numeric value for the GO-level |
organism |
The organism of interest. If NULL the results will be from the general GO BP tree |
A list of GO-terms from the level
The Gene Ontology (GO) biological process (BP) tree was built using the root node GO:0001850
# Gene association GO-terms for organism Yeast on level 6 Level2GOTermBP(level = 6, organism = "Yeast") # Gene association GO-terms for organism Fruit fly on level 2 Level2GOTermBP(level = 2, organism = "Fruit fly")# Gene association GO-terms for organism Yeast on level 6 Level2GOTermBP(level = 6, organism = "Yeast") # Gene association GO-terms for organism Fruit fly on level 2 Level2GOTermBP(level = 2, organism = "Fruit fly")
Gets all the biological process (CC) GO-terms on a GO-level. The supported organisms are "Homo sapiens / Human", "Rattus norvegicus / Rat", "Mus musculus / Mouse", "Danio rerio / Zebrafish", "Caenorhabditis elegans / Worm" ,"Arabidopsis thaliana / Cress", "Saccharomyces cerevisiae / Yeast", "Schizosaccharomyces pombe / Fission yeast", "Drosophila melanogaster / Fruit fly", "Escherichia coli / E.coli".
Level2GOTermCC(level, organism = NULL)Level2GOTermCC(level, organism = NULL)
level |
A numeric value for the GO-level |
organism |
The organism of interest. If NULL the results will be from the general GO CC tree |
A list of GO-terms from the level
The Gene Ontology (GO) cellular component (CC) tree was built using the root node GO:0005575
# Gene association GO-terms for organism Rat on level 4 Level2GOTermCC(level = 4, organism = "Rat") # Gene association GO-terms for the General GO CC tree Level2GOTermCC(level = 7)# Gene association GO-terms for organism Rat on level 4 Level2GOTermCC(level = 4, organism = "Rat") # Gene association GO-terms for the General GO CC tree Level2GOTermCC(level = 7)
Gets all the molecular function (MF) GO-terms on a GO-level. The supported organisms are "Homo sapiens / Human", "Rattus norvegicus / Rat", "Mus musculus / Mouse", "Danio rerio / Zebrafish", "Caenorhabditis elegans / Worm" ,"Arabidopsis thaliana / Cress", "Saccharomyces cerevisiae / Yeast", "Schizosaccharomyces pombe / Fission yeast", "Drosophila melanogaster / Fruit fly", "Escherichia coli / E.coli".
Level2GOTermMF(level, organism = NULL)Level2GOTermMF(level, organism = NULL)
level |
A numeric value for the GO-level |
organism |
The organism of interest. If NULL the results will be from the general GO MF tree |
A list of GO-terms from the level
The Gene Ontology (GO) molecular function (MF) tree was built using the root node GO:0003674
# Gene association GO-terms for organism Mouse on level 9 Level2GOTermMF(level = 9, organism = "mouse") # Gene association GO-terms for organism Zebrafish on level 10 Level2GOTermMF(level = 10, organism = "zebrafish")# Gene association GO-terms for organism Mouse on level 9 Level2GOTermMF(level = 9, organism = "mouse") # Gene association GO-terms for organism Zebrafish on level 10 Level2GOTermMF(level = 10, organism = "zebrafish")
The function retrieves the Jump nodes (JNs) from a GO-level. JNs are those GO-terms which have at least one child term not present in the level below it. If the optional parameter "organism" is missing then the results are from the general GO tree. The supported organisms are "Homo sapiens / Human", "Rattus norvegicus / Rat", "Mus musculus / Mouse", "Danio rerio / Zebrafish", "Caenorhabditis elegans / Worm" ,"Arabidopsis thaliana / cress", "Saccharomyces cerevisiae / Yeast", "Schizosaccharomyces pombe / Fission yeast", "Drosophila melanogaster / Fruit fly", "Escherichia coli / E.coli".
Level2JumpNodeBP(level, organism = NULL)Level2JumpNodeBP(level, organism = NULL)
level |
A numeric value for the GO-level |
organism |
Organism of interest that is supported by the package |
All jump nodes from the level
# Jump nodes from level 3 Level2JumpNodeBP(level = 3, organism = "Homo sapiens") # Jump nodes from level 6 Level2JumpNodeBP(level = 6, organism = "Arabidopsis thaliana")# Jump nodes from level 3 Level2JumpNodeBP(level = 3, organism = "Homo sapiens") # Jump nodes from level 6 Level2JumpNodeBP(level = 6, organism = "Arabidopsis thaliana")
The function retrieves the Jump nodes (JNs) from a GO-level. JNs are those GO-terms which have at least one child term not present in the level below it. If the optional parameter "organism" is missing then the result are from the general GO tree. The supported organisms are "Homo sapiens / Human", "Rattus norvegicus / Rat", "Mus musculus / Mouse", "Danio rerio / Zebrafish", "Caenorhabditis elegans / Worm" ,"Arabidopsis thaliana / Cress", "Saccharomyces cerevisiae / Yeast", "Schizosaccharomyces pombe / Fission yeast", "Drosophila melanogaster / Fruit fly", "Escherichia coli / E.coli".
Level2JumpNodeCC(level, organism = NULL)Level2JumpNodeCC(level, organism = NULL)
level |
A numeric value for the GO-level |
organism |
Organism of interest that is supported by the package |
All jump nodes from the level
# Jump nodes on level 5 Level2JumpNodeCC(level = 5, organism = "Saccharomyces cerevisiae" ) # Jump nodes on level 3 Level2JumpNodeCC(level = 3, organism = "Schizosaccharomyces pombe" )# Jump nodes on level 5 Level2JumpNodeCC(level = 5, organism = "Saccharomyces cerevisiae" ) # Jump nodes on level 3 Level2JumpNodeCC(level = 3, organism = "Schizosaccharomyces pombe" )
The function retrieves the Jump nodes (JNs) from a GO-level. JNs are those GO-terms which have at least one child term not present in the level below it. If the optional parameter "organism" is missing then the results are from the general GO tree. The supported organisms are "Homo sapiens / Human", "Rattus norvegicus / Rat", "Mus musculus / Mouse", "Danio rerio / Zebrafish", "Caenorhabditis elegans / Worm" ,"Arabidopsis thaliana / Cress", "Saccharomyces cerevisiae / Yeast", "Schizosaccharomyces pombe / Fission yeast", "Drosophila melanogaster / Fruit fly", "Escherichia coli / E.coli".
Level2JumpNodeMF(level, organism = NULL)Level2JumpNodeMF(level, organism = NULL)
level |
A numeric value for the GO-level |
organism |
Organism of interest that is supported by the package |
All jump nodes from the level
# Jump nodes on level 3 Level2JumpNodeMF(level = 3, organism = "Danio rerio" ) # Jump nodes on level 6 Level2JumpNodeMF(level = 6, organism = "Caenorhabditis elegans" )# Jump nodes on level 3 Level2JumpNodeMF(level = 3, organism = "Danio rerio" ) # Jump nodes on level 6 Level2JumpNodeMF(level = 6, organism = "Caenorhabditis elegans" )
Derive all the leaf nodes from a GO BP level. The supported organism are "Homo sapiens / Human", "Rattus norvegicus / Rat", "Mus musculus / Mouse", "Danio rerio / Zebrafish", "Caenorhabditis elegans / Worm", "Arabidopsis thaliana / Cress", "Saccharomyces cerevisiae / Yeast", "Schizosaccharomyces pombe / Fission yeast", "Drosophila melanogaster / Fruit fly", "Escherichia coli / E.coli".
Level2LeafNodeBP(level, organism = NULL)Level2LeafNodeBP(level, organism = NULL)
level |
A numeric value for the GO-level |
organism |
An organism of interest from the list of supported organism. If the parameter is NULL the results are from the general GO-DAG (default). |
All leaf nodes on the level.
# level 2 leaf nodes for Drosophila melanogaster GO-DAG Level2LeafNodeBP(2, "Drosophila melanogaster") # level 10 leaf nodes for Drosophila melanogaster GO-DAG Level2LeafNodeBP(10, "Drosophila melanogaster")# level 2 leaf nodes for Drosophila melanogaster GO-DAG Level2LeafNodeBP(2, "Drosophila melanogaster") # level 10 leaf nodes for Drosophila melanogaster GO-DAG Level2LeafNodeBP(10, "Drosophila melanogaster")
Derive all the leaf nodes from a GO CC level. The supported organism are "Homo sapiens / Human", "Rattus norvegicus / Rat", "Mus musculus / Mouse", "Danio rerio / Zebrafish", "Caenorhabditis elegans / Worm", "Arabidopsis thaliana / Cress", "Saccharomyces cerevisiae / Yeast", "Schizosaccharomyces pombe / Fission yeast", "Drosophila melanogaster / Fruit fly", "Escherichia coli / E.coli".
Level2LeafNodeCC(level, organism = NULL)Level2LeafNodeCC(level, organism = NULL)
level |
A numeric value for the GO level |
organism |
An organism of interest from the list of supported organism. If the argument is NULL the results are from the general GO-DAG (default). |
All leaf nodes on the level
# level 6 leaf nodes for Yeast GO-DAG Level2LeafNodeCC(6, "Yeast") # level 4 leaf nodes for Mouse GO-DAG Level2LeafNodeCC(4, "Mouse")# level 6 leaf nodes for Yeast GO-DAG Level2LeafNodeCC(6, "Yeast") # level 4 leaf nodes for Mouse GO-DAG Level2LeafNodeCC(4, "Mouse")
Derive all the leaf nodes from a GO MF level. The supported organism are "Homo sapiens / Human", "Rattus norvegicus / Rat", "Mus musculus / Mouse", "Danio rerio / Zebrafish", "Caenorhabditis elegans / Worm", "Arabidopsis thaliana / Cress", "Saccharomyces cerevisiae / Yeast", "Schizosaccharomyces pombe / Fission yeast", "Drosophila melanogaster / Fruit fly", "Escherichia coli / E.coli".
Level2LeafNodeMF(level, organism = NULL)Level2LeafNodeMF(level, organism = NULL)
level |
A numeric value for the GO-level |
organism |
An organism of interest from the list of supported organism. If NULL the results are from the general GO-DAG (default). |
All leaf nodes on the level
# level 9 leaf nodes for Human GO-DAG Level2LeafNodeMF(9, "Human") # level 5 leaf nodes for Mouse GO-DAG Level2LeafNodeMF(5, "Mouse")# level 9 leaf nodes for Human GO-DAG Level2LeafNodeMF(9, "Human") # level 5 leaf nodes for Mouse GO-DAG Level2LeafNodeMF(5, "Mouse")
This function returns all the non-leaf GO-terms on a particular GO BP level. The supported organism are "Homo sapiens / Human", "Rattus norvegicus / Rat", "Mus musculus / Mouse", "Danio rerio / Zebrafish", "Caenorhabditis elegans / Worm", "Arabidopsis thaliana / Cress", "Saccharomyces cerevisiae / Yeast", "Schizosaccharomyces pombe / Fission yeast", "Drosophila melanogaster / Fruit fly", "Escherichia coli / E.coli"
Level2NoLeafNodeBP(level, organism = NULL)Level2NoLeafNodeBP(level, organism = NULL)
level |
A numeric value for the GO-level |
organism |
The organism of interest from the list of supported organism. If NULL the results are from the general GO-DAG (default) |
A set of non-leaf GO-terms
# Non-leaf nodes from level 13 GO-DAG Level2NoLeafNodeBP(13) # Non-leaf nodes from level 3 for Rat BP GO-DAG Level2NoLeafNodeBP(3, "Rattus norvegicus")# Non-leaf nodes from level 13 GO-DAG Level2NoLeafNodeBP(13) # Non-leaf nodes from level 3 for Rat BP GO-DAG Level2NoLeafNodeBP(3, "Rattus norvegicus")
This function returned all the non-leaf GO terms on a particular GO CC level. The supported organism are "Homo sapiens / Human", "Rattus norvegicus / Rat", "Mus musculus / Mouse", "Danio rerio / Zebrafish", "Caenorhabditis elegans / Worm" ,"Arabidopsis thaliana / Cress", "Saccharomyces cerevisiae / Yeast", "Schizosaccharomyces pombe / Fission yeast", "Drosophila melanogaster / Fruit fly", "Escherichia coli / E.coli"
Level2NoLeafNodeCC(level, organism = NULL)Level2NoLeafNodeCC(level, organism = NULL)
level |
A numeric value for the GO level |
organism |
The organism of interest from the list of supported organism. If NULL the results are from the general GO-DAG (default) |
A set of non-leaf GO terms
# Non-leaf nodes from level 16 for Yeast CC GO-DAG Level2NoLeafNodeCC(level = 16, "Yeast") # Non-leaf nodes from level 10 for Mouse CC GO-DAG Level2NoLeafNodeCC( 10, "Mus musculus")# Non-leaf nodes from level 16 for Yeast CC GO-DAG Level2NoLeafNodeCC(level = 16, "Yeast") # Non-leaf nodes from level 10 for Mouse CC GO-DAG Level2NoLeafNodeCC( 10, "Mus musculus")
This function returned all the non-leaf GO-terms on a particular GO MF level that are not. The supported organisms are "Homo sapiens / Human", "Rattus norvegicus / Rat", "Mus musculus / Mouse", "Danio rerio / Zebrafish", "Caenorhabditis elegans / Worm" ,"Arabidopsis thaliana / Cress", "Saccharomyces cerevisiae / Yeast", "Schizosaccharomyces pombe / Fission yeast", "Drosophila melanogaster / Fruit fly", "Escherichia coli / E.coli".
Level2NoLeafNodeMF(level, organism = NULL)Level2NoLeafNodeMF(level, organism = NULL)
level |
A numeric value for the GO-level |
organism |
The organism of interest from the list of supported organism. If null the results are from the general GO-DAG (default) |
A set of non-leaf GO-terms
# Non-leaf nodes on level 15 Level2NoLeafNodeMF(15) # Non-leaf nodes from level 10 for Rat MF GO-DAG Level2NoLeafNodeMF(10, "Rat")# Non-leaf nodes on level 15 Level2NoLeafNodeMF(15) # Non-leaf nodes from level 10 for Rat MF GO-DAG Level2NoLeafNodeMF(10, "Rat")
The function retrieves the Regular nodes (RNs) from a GO-level. RNs are those GO-terms which have all their children term in the next GO-level (i.e level of parent + 1). If the optional parameter "organism" is missing then the result will be from the general GO tree instead of from a particular organism. The supported organisms are "Homo sapiens / Human", "Rattus norvegicus / Rat", "Mus musculus / Mouse", "Danio rerio / Zebrafish", "Caenorhabditis elegans / Worm" ,"Arabidopsis thaliana / Cress", "Saccharomyces cerevisiae / Yeast", "Schizosaccharomyces pombe / Fission yeast", "Drosophila melanogaster / Fruit fly", "Escherichia coli / E.coli".
Level2RegularNodeBP(level, organism = NULL)Level2RegularNodeBP(level, organism = NULL)
level |
A numeric value for the GO-level |
organism |
Organism of interest that is supported by the package |
Regular nodes from the GO-level
# Regular nodes on level 3 Level2RegularNodeBP(level = 3, organism = "Human" ) # Regular nodes on level 6 Level2RegularNodeBP(level = 6, organism = "Mus musculus" )# Regular nodes on level 3 Level2RegularNodeBP(level = 3, organism = "Human" ) # Regular nodes on level 6 Level2RegularNodeBP(level = 6, organism = "Mus musculus" )
The function retrieves the Regular nodes (RNs) from a GO-level. RNs are those GO-terms which have all their children in the next GO-level (i.e level = level of parent + 1). If the optional parameter "organism" is missing then the result will be from the general GO tree instead of from a particular organism. The supported organisms are "Homo sapiens / Human", "Rattus norvegicus / Rat", "Mus musculus / Mouse", "Danio rerio / Zebrafish", "Caenorhabditis elegans / Worm" ,"Arabidopsis thaliana / Cress", "Saccharomyces cerevisiae / Yeast", "Schizosaccharomyces pombe / Fission yeast", "Drosophila melanogaster / Fruit fly", "Escherichia coli / E.coli".
Level2RegularNodeCC(level, organism = NULL)Level2RegularNodeCC(level, organism = NULL)
level |
A numeric value for the GO-level |
organism |
Organism of interest that is supported by the package |
Regular nodes from the GO-level
# Regualar nodes on level 5 Level2RegularNodeCC(level = 5, organism = "Yeast") # Regular nodes on level 9 Level2RegularNodeCC(level = 9, organism = "Rat")# Regualar nodes on level 5 Level2RegularNodeCC(level = 5, organism = "Yeast") # Regular nodes on level 9 Level2RegularNodeCC(level = 9, organism = "Rat")
The function retrieves the Regular nodes (RNs) from a GO-level. RNs are those GO-terms which have all their children in the next GO-level (i.e level = level of parent + 1). If the optional parameter "organism" is missing then the result will be from the general GO tree instead of from a particular organism. The supported organisms are "Homo sapiens / Human", "Rattus norvegicus / Rat", "Mus musculus / Mouse", "Danio rerio / Zebrafish", "Caenorhabditis elegans / Worm" ,"Arabidopsis thaliana / Cress", "Saccharomyces cerevisiae / Yeast", "Schizosaccharomyces pombe / Fission yeast", "Drosophila melanogaster / Fruit fly", "Escherichia coli / E.coli".
Level2RegularNodeMF(level, organism = NULL)Level2RegularNodeMF(level, organism = NULL)
level |
A numeric value for the GO-level |
organism |
Organism of interest that is supported by the package |
Regular nodes from the GO-level
# Regular nodes on level 3 Level2RegularNodeMF(level = 3, organism = "Human" ) # Regular nodes on level 6 Level2RegularNodeMF(level = 6, organism = "MUS MUSCULUS" )# Regular nodes on level 3 Level2RegularNodeMF(level = 3, organism = "Human" ) # Regular nodes on level 6 Level2RegularNodeMF(level = 6, organism = "MUS MUSCULUS" )
Given a vector of GO-terms, this function prioritizes the GO-terms by expoiting the structure of a DAG. Starting from the GO-term on the highest level and searching all the paths to the root node iteratively. If any GO-terms in the input vector are found along this path, these GO-terms are removed. This is because the GO-term at the end of a path is more specific than the GO-terms along the path. For an organism, the GO-terms of that organism are used for the prioritization. The supported organisms are "Homo sapiens / Human", "Rattus norvegicus / Rat", "Mus musculus / Mouse", "Danio rerio / Zebrafish", "Caenorhabditis elegans / Worm" ,"Arabidopsis thaliana / Cress", "Saccharomyces cerevisiae / Yeast", "Schizosaccharomyces pombe / Fission yeast", "Drosophila melanogaster / Fruit fly", "Escherichia coli / E.coli".
prioritizedGOTerms(lst = NULL, organism = NULL, sp = TRUE, domain = "BP")prioritizedGOTerms(lst = NULL, organism = NULL, sp = TRUE, domain = "BP")
lst |
The GO ids we want to prioritize |
organism |
If organism is given then only the gene association GO-terms of that organism are considered during the prioritization otherwise, all the (non-retired) GO-terms from a particular ontology are used in the ranking. |
sp |
If the argument "sp" is TRUE, only shortest paths are used, otherwise all paths |
domain |
Ontology of the GO-terms. The default is BP. |
A list containing the prioritize GO-terms, their ranking, original GO-terms and their GO-levels is given.
Terms <-c("GO:0000278", "GO:0006414","GO:0022403","GO:0006415","GO:0006614", "GO:0045047","GO:0022411","GO:0001775","GO:0046649","GO:045321") prioritizedGOTerms(Terms, organism = "Human", sp=TRUE, domain = "BP")Terms <-c("GO:0000278", "GO:0006414","GO:0022403","GO:0006415","GO:0006614", "GO:0045047","GO:0022411","GO:0001775","GO:0046649","GO:045321") prioritizedGOTerms(Terms, organism = "Human", sp=TRUE, domain = "BP")
scoreRankingGO provides ranking for a given list of GO-terms according to a score.
scoreRankingGO(goterm, domain = "BP", plot = TRUE)scoreRankingGO(goterm, domain = "BP", plot = TRUE)
goterm |
A list of GO-terms to be ordered |
domain |
The ontology of the GO-terms. The default is "BP" |
plot |
If FALSE the visualisation of the ordering is not provided. The default is TRUE. |
The function returns the ordered GO-terms, the indices corresponding to these GO-terms, the score of each GO-term and a plot of the visualization by default.
goterm <- c( "GO:0000278","GO:0006414","GO:0022403","GO:0006415", "GO:0045047","GO:0072599","GO:0006613","GO:0000184","GO:0070972", "GO:0006413","GO:0000087","GO:0000280","GO:0000279","GO:0006612", "GO:0000956","GO:0048285","GO:0019080","GO:0019083", "GO:0006402","GO:0032984","GO:0006401","GO:0072594","GO:0019058", "GO:0051301","GO:0016071","GO:0006412","GO:0002682","GO:0022411", "GO:0006614") #The GO-terms in the list are ordered according to a score scoreRankingGO(goterm = goterm, domain = "BP", plot = TRUE)goterm <- c( "GO:0000278","GO:0006414","GO:0022403","GO:0006415", "GO:0045047","GO:0072599","GO:0006613","GO:0000184","GO:0070972", "GO:0006413","GO:0000087","GO:0000280","GO:0000279","GO:0006612", "GO:0000956","GO:0048285","GO:0019080","GO:0019083", "GO:0006402","GO:0032984","GO:0006401","GO:0072594","GO:0019058", "GO:0051301","GO:0016071","GO:0006412","GO:0002682","GO:0022411", "GO:0006614") #The GO-terms in the list are ordered according to a score scoreRankingGO(goterm = goterm, domain = "BP", plot = TRUE)
A sub-dag of biological process terms for a certain species e.g DAG of the gene association GO-terms for Arabidopsis thaliana. The label "J","R" and "L" on the right side of the plot gives the number of connections between the regular node (RN) on the level and the nodes right below it (RN are nodes that have all their children nodes represented in the next level) .The supported organisms are "Homo sapiens / Human", "Rattus norvegicus / Rat", "Mus musculus / Mouse", "Danio rerio / Zebrafish", "Caenorhabditis elegans / Worm" ,"Arabidopsis thaliana / Cress", "Saccharomyces cerevisiae / Yeast", "Schizosaccharomyces pombe / Fission yeast", "Drosophila melanogaster / Fruit fly", "Escherichia coli / E.coli".
visRDAGBP(organism, plot = TRUE)visRDAGBP(organism, plot = TRUE)
organism |
The organism supported by the package. Both the scientific / common name of the organism can be use to derive the Sub-DAG. If this argument is "BP" the reduced BP GO-DAG is visualised. |
plot |
If TRUE, both the reduced DAG and the GO-terms contained in each node are derived |
A list containing the plot of the DAG and all the GO terms presents in each node
# Reduced GO-DAG for Human visRDAGBP(organism = "Homo sapiens") # Reduced GO-DAG for Rat visRDAGBP(organism = "Rat") # RN GO-terms on level 2 can be access as follows visRDAGBP(organism = "Human", plot = FALSE)$"L2 RN" # JN GO-terms on level 16 can be access as follows visRDAGBP(organism = "Human", plot = FALSE)$"L16 JN" # LN GO-terms on level 18 can be access as follows visRDAGBP(organism = "Human", plot = FALSE)$"L18 LN"# Reduced GO-DAG for Human visRDAGBP(organism = "Homo sapiens") # Reduced GO-DAG for Rat visRDAGBP(organism = "Rat") # RN GO-terms on level 2 can be access as follows visRDAGBP(organism = "Human", plot = FALSE)$"L2 RN" # JN GO-terms on level 16 can be access as follows visRDAGBP(organism = "Human", plot = FALSE)$"L16 JN" # LN GO-terms on level 18 can be access as follows visRDAGBP(organism = "Human", plot = FALSE)$"L18 LN"
A sub-dag of cellular component terms for a certain species e.g DAG of the gene association terms for Arabidopsis thaliana.The label "J","R" and "L" on the right side of the plot gives the number of connections between the regular node (RN) on the level and the nodes right below it (RN are nodes that have all their children nodes represented in the next level). The supported organisms are "Homo sapiens / human", "Rattus norvegicus / Rat", "Mus musculus / Mouse", "Danio rerio / Zebrafish", "Caenorhabditis elegans / Worm" ,"Arabidopsis thaliana / cress", "Saccharomyces cerevisiae / Yeast", "Schizosaccharomyces pombe / Fission yeast", "Drosophila melanogaster / Fruit fly", "Escherichia coli / E.coli".
visRDAGCC(organism, plot = TRUE)visRDAGCC(organism, plot = TRUE)
organism |
The organism supported by the package. Both the scientific / common name of the organism can be use to derive the Sub-DAG. If this argument is "CC" the general CC GO-DAG is visualised. |
plot |
If TRUE, both the reduced DAG and the GO-terms contained in each node is derived |
A list containing the plot of the DAG and all the GO-terms presents in each node
# Reduced GO-DAG for Arabidopsis thaliana visRDAGCC(organism = "Arabidopsis thaliana") # Reduced GO-DAG for Saccharomyces cerevisiae visRDAGCC(organism = "Worm") # RN GO-terms on level 2 can be access as follows visRDAGCC(organism = "Human", plot = FALSE)$"L2 RN" # JN GO-terms on level 12 can be access as follows visRDAGCC(organism = "Human", plot = FALSE)$"L12 JN" # LN GO-terms on level 16 can be access as follows visRDAGCC(organism = "Human", plot = FALSE)$"L16 LN"# Reduced GO-DAG for Arabidopsis thaliana visRDAGCC(organism = "Arabidopsis thaliana") # Reduced GO-DAG for Saccharomyces cerevisiae visRDAGCC(organism = "Worm") # RN GO-terms on level 2 can be access as follows visRDAGCC(organism = "Human", plot = FALSE)$"L2 RN" # JN GO-terms on level 12 can be access as follows visRDAGCC(organism = "Human", plot = FALSE)$"L12 JN" # LN GO-terms on level 16 can be access as follows visRDAGCC(organism = "Human", plot = FALSE)$"L16 LN"
A sub-dag of molecular function terms for a certain species e.g DAG of the gene association GO-terms for Arabidopsis thaliana. The label "J","R" and "L" on the right side of the plot gives the number of connections between the regular node (RN) on the level and the nodes right below it (RN are nodes that have all their children nodes represented in the next level). The supported organisms are "Homo sapiens / Human", "Rattus norvegicus / Rat", "Mus musculus / Mouse", "Danio rerio / Zebrafish", "Caenorhabditis elegans / Worm" ,"Arabidopsis thaliana / Cress", "Saccharomyces cerevisiae / Yeast", "Schizosaccharomyces pombe / Fission yeast", "Drosophila melanogaster / Fruit fly", "Escherichia coli / E.coli".
visRDAGMF(organism, plot = TRUE)visRDAGMF(organism, plot = TRUE)
organism |
The organism supported by the package. Both the scientific / common name of the organism can be use to derive the Sub-DAG. If this argument is "MF" the reduced MF GO-DAG is visualised. |
plot |
If TRUE, both the reduced DAG and the GO-terms contained in each node is derived |
A list containing the plot of the DAG and all the GO terms presents in each node
# Reduced GO-DAG for Zebrafish visRDAGMF(organism = "Zebrafish") # Reduced GO-DAG for Caenorhabditis elegans visRDAGMF(organism = "Caenorhabditis elegans") # RN GO-terms on level 1 can be access as follows visRDAGMF(organism = "Caenorhabditis elegans", plot = FALSE)$"L1 RN" # JN GO-terms on level 9 can be access as follows visRDAGMF(organism = "Caenorhabditis elegans", plot = FALSE)$"L9 JN" # LN GO-terms on level 14 can be access as follows visRDAGMF(organism = "Caenorhabditis elegans", plot = FALSE)$"L14 LN"# Reduced GO-DAG for Zebrafish visRDAGMF(organism = "Zebrafish") # Reduced GO-DAG for Caenorhabditis elegans visRDAGMF(organism = "Caenorhabditis elegans") # RN GO-terms on level 1 can be access as follows visRDAGMF(organism = "Caenorhabditis elegans", plot = FALSE)$"L1 RN" # JN GO-terms on level 9 can be access as follows visRDAGMF(organism = "Caenorhabditis elegans", plot = FALSE)$"L9 JN" # LN GO-terms on level 14 can be access as follows visRDAGMF(organism = "Caenorhabditis elegans", plot = FALSE)$"L14 LN"
A category in the organism specific DAG is regarded as important if it contains at least one GO-terms from the vector supplied. The function does not visualise the entire organism's DAG, it accepts a range of GO-terms and DAG categories that contains these GO-terms are visualise. We refer to these categories as the important and everything else is faded out. The supported organisms are "Homo sapiens / Human", "Rattus norvegicus / Rat", "Mus musculus / Mouse", "Danio rerio / Zebrafish", "Caenorhabditis elegans / Worm" ,"Arabidopsis thaliana / Cress", "Saccharomyces cerevisiae / Yeast", "Schizosaccharomyces pombe / Fission yeast", "Drosophila melanogaster / Fruit fly", "Escherichia coli / E.coli".
visRsubDAGBP(goterm, organism)visRsubDAGBP(goterm, organism)
goterm |
A vector of biological process GO-terms |
organism |
The organism whose DAG we want to visualise based on the GO-terms supplied. If this argument is "BP" the general reduced GO BP tree is used. |
Returns a plot highlighting the important categories i.e. the categories containing the GO-terms of interest
Terms <- c("GO:0000278", "GO:0006414","GO:0022403","GO:0006415", "GO:0006614","GO:0045047","GO:0072599","GO:0000279") # Visualised Human GO-DAG based on the GO-terms given visRsubDAGBP(goterm = Terms, organism = "Human")Terms <- c("GO:0000278", "GO:0006414","GO:0022403","GO:0006415", "GO:0006614","GO:0045047","GO:0072599","GO:0000279") # Visualised Human GO-DAG based on the GO-terms given visRsubDAGBP(goterm = Terms, organism = "Human")
A category in the organism-specific DAG is regarded as important if it contains at least one GO-terms from the vector given. The function does not visualise the entire organism's DAG, it accepts a range of GO-terms and DAG categories that contains these GO-terms are visualise. We refer to these categories as the important and everything else is faded out. The supported organisms are "Homo sapiens / Human", "Rattus norvegicus / Rat", "Mus musculus / Mouse", "Danio rerio / Zebrafish", "Caenorhabditis elegans / Worm" ,"Arabidopsis thaliana / Cress", "Saccharomyces cerevisiae / Yeast", "Schizosaccharomyces pombe / Fission yeast", "Drosophila melanogaster / Fruit fly", "Escherichia coli / E.coli".
visRsubDAGCC(goterm, organism)visRsubDAGCC(goterm, organism)
goterm |
A vector of cellular component GO-terms |
organism |
The organism whose DAG we want to visualise based on the GO-terms supplied |
Returns a plot highlighting the important categories i.e. the categories containing the GO-terms of interest. If this argument is "CC" the general reduced GO CC tree is used.
# Visualised Human GO-DAG based on the GO-terms given Terms <- c("GO:0030054","GO:0045171","GO:0043204") visRsubDAGCC(goterm = Terms, organism = "Human")# Visualised Human GO-DAG based on the GO-terms given Terms <- c("GO:0030054","GO:0045171","GO:0043204") visRsubDAGCC(goterm = Terms, organism = "Human")
A category in the organism-specific DAG is regarded as important if it contains at least one GO-terms from the vector supplied. The function does not visualise the entire organism's DAG, it accepts a range of GO-terms and DAG categories that contains these GO-terms are visualise. We refer to these categories as the important and everything else is faded out. The supported organisms are "Homo sapiens / Human", "Rattus norvegicus / Rat", "Mus musculus / Mouse", "Danio rerio / Zebrafish", "Caenorhabditis elegans / Worm" ,"Arabidopsis thaliana / Cress", "Saccharomyces cerevisiae / Yeast", "Schizosaccharomyces pombe / Fission yeast", "Drosophila melanogaster / Fruit fly", "Escherichia coli / E.coli".
visRsubDAGMF(goterm, organism)visRsubDAGMF(goterm, organism)
goterm |
A vector of molecular function GO-terms |
organism |
The organism whose DAG we want to visualise based on the GO-terms supplied. If this argument is "MF" the general reduced GO MF tree is used. |
Returns a plot highlighting the important categories i.e. the categories containing the GO-terms of interest
Terms <- c("GO:0034040","GO:0008374" ,"GO:0003777","GO:0003674","GO:0015440","GO:0005464") visRsubDAGMF(Terms, "Human")Terms <- c("GO:0034040","GO:0008374" ,"GO:0003777","GO:0003674","GO:0015440","GO:0005464") visRsubDAGMF(Terms, "Human")