bioconductor v3.9.0 ClusterProfiler
This package implements methods to analyze and visualize
Link to this section Summary
Functions
Datasets gcSample contains a sample of gene clusters.
GSEA
Gff2GeneTable
KEGG_path2extid
bitr
bitr_kegg
browseKEGG
buildGOmap
statistical analysis and visualization of functional profiles for genes and gene clusters The package implements methods to analyze and visualize functional profiles of gene and gene clusters.
Compare gene clusters functional profile
Class "compareClusterResult" This class represents the comparison result of gene clusters by GO categories at specific level or GO enrichment analysis.
dotplot
download_KEGG
dropGO
enrichDAVID
GO Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment GO categories after FDR control.
KEGG Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment KEGG categories with FDR control.
KEGG Module Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment KEGG Module categories with FDR control.
enricher
fortify
get GOIDs at a specific level
go2ont
go2term
gofilter
Functional Profile of a gene set at specific GO level. Given a vector of genes, this function will return the GO profile at a specific level.
Class "groupGOResult" This class represents the result of functional Profiles of a set of gene at specific GO level.
gseGO
gseKEGG
gseMKEGG
idType
ko2name
merge_result
plotGOgraph
plotting-clusterProfile
read.gmt
Objects exported from other packages
search_kegg_organism
simplify method
uniprot_get
viewKEGG function is for visualize KEGG pathways works with enrichResult object to visualize enriched KEGG pathway
Link to this section Functions
DataSet()
Datasets gcSample contains a sample of gene clusters.
Description
Datasets gcSample contains a sample of gene clusters.
Datasets kegg_species contains kegg species information
GSEA()
GSEA
Description
a universal gene set enrichment analysis tools
Usage
GSEA(geneList, exponent = 1, nPerm = 1000, minGSSize = 10,
maxGSSize = 500, pvalueCutoff = 0.05, pAdjustMethod = "BH",
TERM2GENE, TERM2NAME = NA, verbose = TRUE, seed = FALSE,
by = "fgsea")Arguments
| Argument | Description |
|---|---|
geneList | order ranked geneList |
exponent | weight of each step |
nPerm | number of permutations |
minGSSize | minimal size of each geneSet for analyzing |
maxGSSize | maximal size of genes annotated for testing |
pvalueCutoff | pvalue cutoff |
pAdjustMethod | p value adjustment method |
TERM2GENE | user input annotation of TERM TO GENE mapping, a data.frame of 2 column with term and gene |
TERM2NAME | user input of TERM TO NAME mapping, a data.frame of 2 column with term and name |
verbose | logical |
seed | logical |
by | one of 'fgsea' or 'DOSE' |
Value
gseaResult object
Author
Guangchuang Yu
Gff2GeneTable()
Gff2GeneTable
Description
read GFF file and build gene information table
Usage
Gff2GeneTable(gffFile, compress = TRUE)Arguments
| Argument | Description |
|---|---|
gffFile | GFF file |
compress | compress file or not |
Details
given a GFF file, this function extracts information from it and save it in working directory
Value
file save.
Author
Yu Guangchuang
KEGG_path2extid()
KEGG_path2extid
Description
query all genes in a KEGG pathway or module
Usage
KEGG_path2extid(keggID, species = sub("\d+$", "", keggID),
keggType = "Path", keyType = "kegg")Arguments
| Argument | Description |
|---|---|
keggID | KEGG ID, path or module ID |
species | species |
keggType | one of 'Path' or 'Module' |
keyType | KEGG gene type, one of "ncbi-proteinid", "ncbi-geneid", "uniprot", or "kegg" |
Value
extid vector
Author
guangchuang yu
bitr()
bitr
Description
Biological Id TRanslator
Usage
bitr(geneID, fromType, toType, OrgDb, drop = TRUE)Arguments
| Argument | Description |
|---|---|
geneID | input gene id |
fromType | input id type |
toType | output id type |
OrgDb | annotation db |
drop | drop NA or not |
Value
data.frame
Author
Guangchuang Yu
bitr_kegg()
bitr_kegg
Description
convert biological ID using KEGG API
Usage
bitr_kegg(geneID, fromType, toType, organism, drop = TRUE)Arguments
| Argument | Description |
|---|---|
geneID | input gene id |
fromType | input id type |
toType | output id type |
organism | supported organism, can be search using search_kegg_organism function |
drop | drop NA or not |
Value
data.frame
Author
Guangchuang Yu
browseKEGG()
browseKEGG
Description
open KEGG pathway with web browser
Usage
browseKEGG(x, pathID)Arguments
| Argument | Description |
|---|---|
x | an instance of enrichResult or gseaResult |
pathID | pathway ID |
Value
url
Author
Guangchuang Yu
buildGOmap()
buildGOmap
Description
building GO mapping files
Usage
buildGOmap(gomap)Arguments
| Argument | Description |
|---|---|
gomap | data.frame with two columns of GO and gene ID |
Details
provided by a data.frame of GO (column 1) and gene (column 2) direct annotation this function will building gene to GO and GO to gene mapping, with directly and undirectly (ancestor GO term) annotation.
Value
data.frame, GO annotation with indirect annotation
Author
Yu Guangchuang
clusterProfiler_package()
statistical analysis and visualization of functional profiles for genes and gene clusters The package implements methods to analyze and visualize functional profiles of gene and gene clusters.
Description
statistical analysis and visualization of functional profiles for genes and gene clusters The package implements methods to analyze and visualize functional profiles of gene and gene clusters.
compareCluster()
Compare gene clusters functional profile
Description
Given a list of gene set, this function will compute profiles of each gene cluster.
Usage
compareCluster(geneClusters, fun = "enrichGO", data = "", ...)Arguments
| Argument | Description |
|---|---|
geneClusters | a list of entrez gene id. Alternatively, a formula of type Entrez~group |
fun | One of "groupGO", "enrichGO", "enrichKEGG", "enrichDO" or "enrichPathway" . |
data | if geneClusters is a formula, the data from which the clusters must be extracted. |
... | Other arguments. |
Value
A clusterProfResult instance.
Seealso
compareClusterResult-class , groupGO
enrichGO
Author
Guangchuang Yu https://guangchuangyu.github.io
Examples
data(gcSample)
xx <- compareCluster(gcSample, fun="enrichKEGG",
organism="hsa", pvalueCutoff=0.05)
as.data.frame(xx)
# plot(xx, type="dot", caption="KEGG Enrichment Comparison")
## formula interface
mydf <- data.frame(Entrez=c('1', '100', '1000', '100101467',
'100127206', '100128071'),
group = c('A', 'A', 'A', 'B', 'B', 'B'),
othergroup = c('good', 'good', 'bad', 'bad', 'good', 'bad'))
xx.formula <- compareCluster(Entrez~group, data=mydf,
fun='groupGO', OrgDb='org.Hs.eg.db')
as.data.frame(xx.formula)
## formula interface with more than one grouping variable
xx.formula.twogroups <- compareCluster(Entrez~group+othergroup, data=mydf,
fun='groupGO', OrgDb='org.Hs.eg.db')
as.data.frame(xx.formula.twogroups)compareClusterResult_class()
Class "compareClusterResult" This class represents the comparison result of gene clusters by GO categories at specific level or GO enrichment analysis.
Description
Class "compareClusterResult" This class represents the comparison result of gene clusters by GO categories at specific level or GO enrichment analysis.
Seealso
groupGOResult
enrichResult compareCluster
Author
Guangchuang Yu https://guangchuangyu.github.io
dotplot_methods()
dotplot
Description
dot plot method
Usage
list(list("dotplot"), list("compareClusterResult"))(object, x = ~Cluster,
color = "p.adjust", showCategory = 5, split = NULL,
font.size = 12, title = "", by = "geneRatio", includeAll = TRUE)Arguments
| Argument | Description |
|---|---|
object | compareClusterResult object |
x | x variable |
color | one of pvalue or p.adjust |
showCategory | category numbers |
split | ONTOLOGY or NULL |
font.size | font size |
title | figure title |
by | one of geneRatio, Percentage or count |
includeAll | logical |
download_KEGG()
download_KEGG
Description
download the latest version of KEGG pathway/module
Usage
download_KEGG(species, keggType = "KEGG", keyType = "kegg")Arguments
| Argument | Description |
|---|---|
species | species |
keggType | one of 'KEGG' or 'MKEGG' |
keyType | supported keyType, see bitr_kegg |
Value
list
Author
Guangchuang Yu
dropGO()
dropGO
Description
drop GO term of specific level or specific terms (mostly too general).
Usage
dropGO(x, level = NULL, term = NULL)Arguments
| Argument | Description |
|---|---|
x | an instance of 'enrichResult' or 'compareClusterResult' |
level | GO level |
term | GO term |
Value
modified version of x
Author
Guangchuang Yu
enrichDAVID()
enrichDAVID
Description
enrichment analysis by DAVID
Usage
enrichDAVID(gene, idType = "ENTREZ_GENE_ID", universe, minGSSize = 10,
maxGSSize = 500, annotation = "GOTERM_BP_FAT", pvalueCutoff = 0.05,
pAdjustMethod = "BH", qvalueCutoff = 0.2, species = NA, david.user)Arguments
| Argument | Description |
|---|---|
gene | input gene |
idType | id type |
universe | background genes |
minGSSize | minimal size of genes annotated for testing |
maxGSSize | maximal size of genes annotated for testing |
annotation | david annotation |
pvalueCutoff | pvalueCutoff |
pAdjustMethod | one of "BH" and "bonferroni" |
qvalueCutoff | qvalutCutoff |
species | species |
david.user | david user |
Value
A enrichResult instance
Author
Guangchuang Yu
enrichGO()
GO Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment GO categories after FDR control.
Description
GO Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment GO categories after FDR control.
Usage
enrichGO(gene, OrgDb, keyType = "ENTREZID", ont = "MF",
pvalueCutoff = 0.05, pAdjustMethod = "BH", universe,
qvalueCutoff = 0.2, minGSSize = 10, maxGSSize = 500,
readable = FALSE, pool = FALSE)Arguments
| Argument | Description |
|---|---|
gene | a vector of entrez gene id. |
OrgDb | OrgDb |
keyType | keytype of input gene |
ont | One of "BP", "MF", and "CC" subontologies, or "ALL" for all three. |
pvalueCutoff | Cutoff value of pvalue. |
pAdjustMethod | one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none" |
universe | background genes |
qvalueCutoff | qvalue cutoff |
minGSSize | minimal size of genes annotated by Ontology term for testing. |
maxGSSize | maximal size of genes annotated for testing |
readable | whether mapping gene ID to gene Name |
pool | If ont='ALL', whether pool 3 GO sub-ontologies |
Value
An enrichResult instance.
Seealso
enrichResult-class , compareCluster
Author
Guangchuang Yu https://guangchuangyu.github.io
Examples
data(geneList, package = "DOSE")
de <- names(geneList)[1:100]
yy <- enrichGO(de, 'org.Hs.eg.db', ont="BP", pvalueCutoff=0.01)
head(yy)enrichKEGG()
KEGG Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment KEGG categories with FDR control.
Description
KEGG Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment KEGG categories with FDR control.
Usage
enrichKEGG(gene, organism = "hsa", keyType = "kegg",
pvalueCutoff = 0.05, pAdjustMethod = "BH", universe,
minGSSize = 10, maxGSSize = 500, qvalueCutoff = 0.2,
use_internal_data = FALSE)Arguments
| Argument | Description |
|---|---|
gene | a vector of entrez gene id. |
organism | supported organism listed in 'http://www.genome.jp/kegg/catalog/org_list.html' |
keyType | one of "kegg", 'ncbi-geneid', 'ncib-proteinid' and 'uniprot' |
pvalueCutoff | Cutoff value of pvalue. |
pAdjustMethod | one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none" |
universe | background genes |
minGSSize | minimal size of genes annotated by Ontology term for testing. |
maxGSSize | maximal size of genes annotated for testing |
qvalueCutoff | qvalue cutoff |
use_internal_data | logical, use KEGG.db or latest online KEGG data |
Value
A enrichResult instance.
Seealso
enrichResult-class , compareCluster
Author
Guangchuang Yu http://ygc.name
Examples
data(geneList, package='DOSE')
de <- names(geneList)[1:100]
yy <- enrichKEGG(de, pvalueCutoff=0.01)
head(yy)enrichMKEGG()
KEGG Module Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment KEGG Module categories with FDR control.
Description
KEGG Module Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment KEGG Module categories with FDR control.
Usage
enrichMKEGG(gene, organism = "hsa", keyType = "kegg",
pvalueCutoff = 0.05, pAdjustMethod = "BH", universe,
minGSSize = 10, maxGSSize = 500, qvalueCutoff = 0.2)Arguments
| Argument | Description |
|---|---|
gene | a vector of entrez gene id. |
organism | supported organism listed in 'http://www.genome.jp/kegg/catalog/org_list.html' |
keyType | one of "kegg", 'ncbi-geneid', 'ncib-proteinid' and 'uniprot' |
pvalueCutoff | Cutoff value of pvalue. |
pAdjustMethod | one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none" |
universe | background genes |
minGSSize | minimal size of genes annotated by Ontology term for testing. |
maxGSSize | maximal size of genes annotated for testing |
qvalueCutoff | qvalue cutoff |
Value
A enrichResult instance.
enricher()
enricher
Description
A universal enrichment analyzer
Usage
enricher(gene, pvalueCutoff = 0.05, pAdjustMethod = "BH", universe,
minGSSize = 10, maxGSSize = 500, qvalueCutoff = 0.2, TERM2GENE,
TERM2NAME = NA)Arguments
| Argument | Description |
|---|---|
gene | a vector of gene id |
pvalueCutoff | pvalue cutoff |
pAdjustMethod | one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none" |
universe | background genes |
minGSSize | minimal size of genes annotated for testing |
maxGSSize | maximal size of genes annotated for testing |
qvalueCutoff | qvalue cutoff |
TERM2GENE | user input annotation of TERM TO GENE mapping, a data.frame of 2 column with term and gene |
TERM2NAME | user input of TERM TO NAME mapping, a data.frame of 2 column with term and name |
Value
A enrichResult instance
Author
Guangchuang Yu
fortify()
fortify
Description
convert compareClusterResult to a data.frame that ready for plot
Usage
list(list("fortify"), list("compareClusterResult"))(model, data, showCategory = 5,
by = "geneRatio", split = NULL, includeAll = TRUE)Arguments
| Argument | Description |
|---|---|
model | compareClusterResult object |
data | not use here |
showCategory | category numbers |
by | one of geneRatio, Percentage or count |
split | ONTOLOGY or NULL |
includeAll | logical |
Value
data.frame
Author
Guangchuang Yu
getGOLevel()
get GOIDs at a specific level
Description
query GOIDs at a specific level.
Usage
getGOLevel(ont, level)Arguments
| Argument | Description |
|---|---|
ont | Ontology |
level | GO level |
Value
a vector of GOIDs
Author
Guangchuang Yu http://guangchuangyu.github.io
go2ont()
go2ont
Description
convert goid to ontology (BP, CC, MF)
Usage
go2ont(goid)Arguments
| Argument | Description |
|---|---|
goid | a vector of GO IDs |
Value
data.frame
Author
Guangchuang Yu
go2term()
go2term
Description
convert goid to descriptive term
Usage
go2term(goid)Arguments
| Argument | Description |
|---|---|
goid | a vector of GO IDs |
Value
data.frame
Author
Guangchuang Yu
gofilter()
gofilter
Description
filter GO enriched result at specific level
Usage
gofilter(x, level = 4)Arguments
| Argument | Description |
|---|---|
x | output from enrichGO or compareCluster |
level | GO level |
Value
updated object
Author
Guangchuang Yu
groupGO()
Functional Profile of a gene set at specific GO level. Given a vector of genes, this function will return the GO profile at a specific level.
Description
Functional Profile of a gene set at specific GO level. Given a vector of genes, this function will return the GO profile at a specific level.
Usage
groupGO(gene, OrgDb, keyType = "ENTREZID", ont = "CC", level = 2,
readable = FALSE)Arguments
| Argument | Description |
|---|---|
gene | a vector of entrez gene id. |
OrgDb | OrgDb |
keyType | key type of input gene |
ont | One of "MF", "BP", and "CC" subontologies. |
level | Specific GO Level. |
readable | if readable is TRUE, the gene IDs will mapping to gene symbols. |
Value
A groupGOResult instance.
Seealso
groupGOResult-class , compareCluster
Author
Guangchuang Yu http://ygc.name
Examples
data(gcSample)
yy <- groupGO(gcSample[[1]], 'org.Hs.eg.db', ont="BP", level=2)
head(summary(yy))
#plot(yy)groupGOResult_class()
Class "groupGOResult" This class represents the result of functional Profiles of a set of gene at specific GO level.
Description
Class "groupGOResult" This class represents the result of functional Profiles of a set of gene at specific GO level.
Seealso
compareClusterResult
compareCluster groupGO
Author
Guangchuang Yu https://guangchuangyu.github.io
gseGO()
gseGO
Description
Gene Set Enrichment Analysis of Gene Ontology
Usage
gseGO(geneList, ont = "BP", OrgDb, keyType = "ENTREZID",
exponent = 1, nPerm = 1000, minGSSize = 10, maxGSSize = 500,
pvalueCutoff = 0.05, pAdjustMethod = "BH", verbose = TRUE,
seed = FALSE, by = "fgsea")Arguments
| Argument | Description |
|---|---|
geneList | order ranked geneList |
ont | one of "BP", "MF", and "CC" subontologies, or "ALL" for all three. |
OrgDb | OrgDb |
keyType | keytype of gene |
exponent | weight of each step |
nPerm | permutation numbers |
minGSSize | minimal size of each geneSet for analyzing |
maxGSSize | maximal size of genes annotated for testing |
pvalueCutoff | pvalue Cutoff |
pAdjustMethod | pvalue adjustment method |
verbose | print message or not |
seed | logical |
by | one of 'fgsea' or 'DOSE' |
Value
gseaResult object
Author
Yu Guangchuang
gseKEGG()
gseKEGG
Description
Gene Set Enrichment Analysis of KEGG
Usage
gseKEGG(geneList, organism = "hsa", keyType = "kegg", exponent = 1,
nPerm = 1000, minGSSize = 10, maxGSSize = 500,
pvalueCutoff = 0.05, pAdjustMethod = "BH", verbose = TRUE,
use_internal_data = FALSE, seed = FALSE, by = "fgsea")Arguments
| Argument | Description |
|---|---|
geneList | order ranked geneList |
organism | supported organism listed in 'http://www.genome.jp/kegg/catalog/org_list.html' |
keyType | one of "kegg", 'ncbi-geneid', 'ncib-proteinid' and 'uniprot' |
exponent | weight of each step |
nPerm | permutation numbers |
minGSSize | minimal size of each geneSet for analyzing |
maxGSSize | maximal size of genes annotated for testing |
pvalueCutoff | pvalue Cutoff |
pAdjustMethod | pvalue adjustment method |
verbose | print message or not |
use_internal_data | logical, use KEGG.db or latest online KEGG data |
seed | logical |
by | one of 'fgsea' or 'DOSE' |
Value
gseaResult object
Author
Yu Guangchuang
gseMKEGG()
gseMKEGG
Description
Gene Set Enrichment Analysis of KEGG Module
Usage
gseMKEGG(geneList, organism = "hsa", keyType = "kegg", exponent = 1,
nPerm = 1000, minGSSize = 10, maxGSSize = 500,
pvalueCutoff = 0.05, pAdjustMethod = "BH", verbose = TRUE,
seed = FALSE, by = "fgsea")Arguments
| Argument | Description |
|---|---|
geneList | order ranked geneList |
organism | supported organism listed in 'http://www.genome.jp/kegg/catalog/org_list.html' |
keyType | one of "kegg", 'ncbi-geneid', 'ncib-proteinid' and 'uniprot' |
exponent | weight of each step |
nPerm | permutation numbers |
minGSSize | minimal size of each geneSet for analyzing |
maxGSSize | maximal size of genes annotated for testing |
pvalueCutoff | pvalue Cutoff |
pAdjustMethod | pvalue adjustment method |
verbose | print message or not |
seed | logical |
by | one of 'fgsea' or 'DOSE' |
Value
gseaResult object
Author
Yu Guangchuang
idType()
idType
Description
list ID types supported by annoDb
Usage
idType(OrgDb = "org.Hs.eg.db")Arguments
| Argument | Description |
|---|---|
OrgDb | annotation db |
Value
character vector
Author
Guangchuang Yu
ko2name()
ko2name
Description
convert ko ID to descriptive name
Usage
ko2name(ko)Arguments
| Argument | Description |
|---|---|
ko | ko ID |
Value
data.frame
Author
guangchuang yu
merge_result()
merge_result
Description
merge a list of enrichResult objects to compareClusterResult
Usage
merge_result(enrichResultList)Arguments
| Argument | Description |
|---|---|
enrichResultList | a list of enrichResult objects |
Value
a compareClusterResult instance
Author
Guangchuang Yu
plotGOgraph()
plotGOgraph
Description
plot GO graph
Usage
plotGOgraph(x, firstSigNodes = 10, useInfo = "all", sigForAll = TRUE,
useFullNames = TRUE, ...)Arguments
| Argument | Description |
|---|---|
x | output of enrichGO or gseGO |
firstSigNodes | number of significant nodes (retangle nodes in the graph) |
useInfo | additional info |
sigForAll | if TRUE the score/p-value of all nodes in the DAG is shown, otherwise only score will be shown |
useFullNames | logical |
... | additional parameter of showSigOfNodes, please refer to topGO |
Value
GO DAG graph
Author
Guangchuang Yu
plottingclusterProfile()
plotting-clusterProfile
Description
Internal plot function for plotting compareClusterResult
Usage
plotting.clusterProfile(clProf.reshape.df, x = ~Cluster, type = "dot",
colorBy = "p.adjust", by = "geneRatio", title = "",
font.size = 12)Arguments
| Argument | Description |
|---|---|
clProf.reshape.df | data frame of compareCluster result |
x | x variable |
type | one of dot and bar |
colorBy | one of pvalue or p.adjust |
by | one of percentage and count |
title | graph title |
font.size | graph font size |
Value
ggplot object
Author
Guangchuang Yu https://guangchuangyu.github.io
readgmt()
read.gmt
Description
parse gmt file to a data.frame
Usage
read.gmt(gmtfile)Arguments
| Argument | Description |
|---|---|
gmtfile | gmt file |
Value
data.frame
Author
Guangchuang Yu
reexports()
Objects exported from other packages
Description
These objects are imported from other packages. Follow the links below to see their documentation.
list(" ", " ", list(list("DOSE"), list(list(list("geneID")), ", ", list(list("geneInCategory")), ", ", list(list("gsfilter")), ", ", list(list("setReadable")))), " ", " ", " ", list(list("enrichplot"), list(list(list("cnetplot")), ", ", list(list("dotplot")), ", ", list(list("emapplot")), ", ", list(list("goplot")), ", ", list(list("gseaplot")), ", ", list(list("heatplot")), ", ", list(list("ridgeplot")))), " ")
search_kegg_organism()
search_kegg_organism
Description
search kegg organism, listed in http://www.genome.jp/kegg/catalog/org_list.html
Usage
search_kegg_organism(str, by = "scientific_name", ignore.case = FALSE)Arguments
| Argument | Description |
|---|---|
str | string |
by | one of 'kegg.code', 'scientific_name' and 'common_name' |
ignore.case | TRUE or FALSE |
Value
data.frame
Author
Guangchuang Yu
simplify_methods()
simplify method
Description
simplify output from enrichGO and gseGO by removing redundancy of enriched GO terms
simplify output from compareCluster by removing redundancy of enriched GO terms
Usage
list(list("simplify"), list("enrichResult"))(x, cutoff = 0.7, by = "p.adjust",
select_fun = min, measure = "Wang", semData = NULL)
list(list("simplify"), list("gseaResult"))(x, cutoff = 0.7, by = "p.adjust",
select_fun = min, measure = "Wang", semData = NULL)
list(list("simplify"), list("compareClusterResult"))(x, cutoff = 0.7,
by = "p.adjust", select_fun = min, measure = "Wang",
semData = NULL)Arguments
| Argument | Description |
|---|---|
x | output of enrichGO |
cutoff | similarity cutoff |
by | feature to select representative term, selected by 'select_fun' function |
select_fun | function to select feature passed by 'by' parameter |
measure | method to measure similarity |
semData | GOSemSimDATA object |
Value
updated enrichResult object
updated compareClusterResult object
Author
Guangchuang Yu
Gwang-Jin Kim and Guangchuang Yu
Guangchuang Yu
References
issue #28 https://github.com/GuangchuangYu/clusterProfiler/issues/28
issue #162 https://github.com/GuangchuangYu/clusterProfiler/issues/162
uniprot_get()
uniprot_get
Description
retreve annotation data from uniprot
Usage
uniprot_get(taxID)Arguments
| Argument | Description |
|---|---|
taxID | taxonomy ID |
Value
gene table data frame
Author
guangchuang yu
viewKEGG()
viewKEGG function is for visualize KEGG pathways works with enrichResult object to visualize enriched KEGG pathway
Description
viewKEGG function is for visualize KEGG pathways works with enrichResult object to visualize enriched KEGG pathway
Usage
viewKEGG(obj, pathwayID, foldChange, color.low = "green",
color.high = "red", kegg.native = TRUE,
out.suffix = "clusterProfiler")Arguments
| Argument | Description |
|---|---|
obj | enrichResult object |
pathwayID | pathway ID or index |
foldChange | fold change values |
color.low | color of low foldChange genes |
color.high | color of high foldChange genes |
kegg.native | logical |
out.suffix | suffix of output file |
References
Luo et al. (2013) Pathview: an R/Bioconductor package for pathway-based data integration and visualization. Bioinformatics (Oxford, England), 29:14 1830--1831, 2013. ISSN 1367-4803 http://bioinformatics.oxfordjournals.org/content/abstract/29/14/1830.abstract PMID: 23740750