getTopGeneSets: Select top significant gene sets from results of GSCA object

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. This function selects top significant gene sets from results of an GSCA object for user-specified gene collections. If 'ntop' is given, then top 'ntop' significant gene sets in gene set collections 'gscs' will be selected and their names will be returned. If 'allSig=TRUE', then all significant (adjusted p-value < 'pValueCutoff' see help("analyze")) gene sets will be selected and their names will be returned.

Usage

## S4 method for signature 'GSCA'
getTopGeneSets(object, resultName, gscs, ntop = NULL, allSig = FALSE)

Arguments

object	A GSCA object.
resultName	A single character value: 'HyperGeo.results' or 'GSEA.results'.
gscs	A character vector specifying the names of gene set collections from which the top significant gene sets will be selected.
ntop	A single integer or numeric value specifying to select how many gene sets of top significance.
allSig	A single logical value. If 'TRUE', all significant gene sets (adjusted p-value < 'pValueCutoff' of slot 'para') will be selected regardless of 'ntop'; otherwise, only top 'ntop' gene sets will be selected.

Value

A named list of character vectors, each element contains the names of top significant gene sets for each gene set collection.

Examples

## load a GSCA object(see the examples of analyze GSCA for details)
data(d7_gsca)

summarize(d7_gsca)
## print top significant gene sets in GO_MF
topGS_GO_MF <- getTopGeneSets(d7_gsca, "GSEA.results", gscs = "GO_MF", allSig=TRUE)

## print top significant gene sets in GO_MF and PW_KEGG
topGS <- getTopGeneSets(d7_gsca, "GSEA.results", gscs = c("GO_MF", "PW_KEGG"), allSig=TRUE)

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