appendGSTerms: Append gene set terms to GSCA results and gene names...

In CityUHK-CompBio/HTSanalyzeR2: HTSanalyzeR2: An R package for functional annotation, network analysis and time series analysis of high-throughput data

Description

This is a generic function. When implemented as the S4 method for objects of class GSCA, this function finds corresponding annotation terms for GO, KEGG and MSigDB gene sets and inserts a column named "Gene.Set.Term" to each data frame in the GSCA results. In the same time, to make results more understandable, it will annotate the gene list with EntrezID to gene symbol under specific species.

Usage

## S4 method for signature 'GSCA'
appendGSTerms(
  object,
  keggGSCs = NULL,
  goGSCs = NULL,
  msigdbGSCs = NULL,
  species = "Hs"
)

Arguments

object	A GSCA object.
keggGSCs	A character vector of names of all KEGG gene set collections.
goGSCs	A character vector of names of all GO gene set collections.
msigdbGSCs	A character vector of names of all MSigDB gene set collections.
species	A single character value specifying the species of the analyzed data. It supports all the species of OrgDb objects in AnnotationDbi. The format should be an abbreviation of the organism as setted by AnnotationDbi. For example, the commonly used ones are "Dm" ("Drosophila_melanogaster"), "Hs" ("Homo_sapiens"), "Rn" ("Rattus_norvegicus"), "Mm" ("Mus_musculus"), "Ce" ("Caenorhabditis_elegans"), and etc.

Details

This function makes the GSCA results more readable by appending a column of terms for KEGG and GO gene sets. To do this, the user needs to specify the names of the gene set collections based on GO, KEGG and MSigDB respectively. In the same time, to make results more understandable, it will annotate the gene list with EntrezID to gene symbol under specific species.

For each GO gene set, the GO id will be mapped to corresponding GO term by the function mapIds of the package AnnotationDbi.

For each KEGG gene set, the species code in the KEGG id will be trimmed off, and then mapped to its corresponding annotation term using the package KEGGREST.

For each MSigDB gene set, the corresponding annotation terms are based on the built-in database in this package.

Value

In the end, this function will return an updated object of class GSCA.

Examples

library(org.Hs.eg.db)
library(GO.db)
library(KEGGREST)
## load data for enrichment analyses
data(d7)
phenotype <- as.vector(d7$neg.lfc)
names(phenotype) <- d7$id

## select hits if you also want to do GSOA, otherwise ignore it
hits <-  names(phenotype[which(abs(phenotype) > 2)])

## set up a list of gene set collections
GO_MF <- GOGeneSets(species="Hs", ontologies=c("MF"))
PW_KEGG <- KeggGeneSets(species="Hs")
ListGSC <- list(GO_MF=GO_MF, PW_KEGG=PW_KEGG)

## create an object of class 'GSCA'
gsca <- GSCA(listOfGeneSetCollections = ListGSC, geneList = phenotype, hits = hits)

## do preprocessing
gsca1 <- preprocess(gsca, species="Hs", initialIDs="SYMBOL", keepMultipleMappings=TRUE,
                   duplicateRemoverMethod="max", orderAbsValue=FALSE)

## support parallel calculation using doParallel package
if (requireNamespace("doParallel", quietly=TRUE)) {
doParallel::registerDoParallel(cores=2)
} else {
}

## do hypergeometric tests and GSEA
gsca2 <- analyze(gsca1, para=list(pValueCutoff=0.01, pAdjustMethod ="BH",
                                nPermutations=100, minGeneSetSize=10, exponent=1),
                                doGSOA = TRUE, doGSEA = TRUE)

## summarize gsca2
summarize(gsca2)
head(getResult(gsca2)$GSEA.results$GO_MF)

## append gene set terms to results and annotate gene list
gsca3 <- appendGSTerms(gsca2, goGSCs=c("GO_MF"),
                       keggGSCs=c("PW_KEGG"), msigdbGSCs=NULL,
                       species = "Hs")
head(getResult(gsca3)$GSEA.results$GO_MF)

CityUHK-CompBio/HTSanalyzeR2 documentation built on Dec. 3, 2020, 2:35 a.m.