EGSEA (version 1.0.3)

topSets: Table of Top Gene Sets from an EGSEA Analysis

Description

Extract a table of the top-ranked gene sets from an EGSEA analysis.

Usage

topSets(gsa, contrast = 1, gs.label = 1, sort.by = NULL, number = 10, names.only = TRUE)

Arguments

gsa

list, the analysis result object from egsea, egsea.cnt or egsea.ora.

contrast

contrast column number or column name specifying which contrast is of interest. if contrast = 0 or "comparison" and the number of contrasts greater than 1, the comparative gene sets are retruned.

gs.label

the number or label of the gene set collection of interest.

sort.by

character, determines how to order the analysis results in the stats table. The accepted values depend on the function used to generate the EGSEA results.

number

integer, maximum number of gene sets to list

names.only

logical, whether to display the EGSEA statistics or not.

Value

A dataframe of top gene sets with the calculated statistics for each if names.only = FALSE.

Examples

library(EGSEAdata)
data(il13.data)
v = il13.data$voom
contrasts = il13.data$contra
gs.annots = buildIdxEZID(entrezIDs=rownames(v$E), species="human", 
msigdb.gsets="none", 
         kegg.updated=FALSE, kegg.exclude = c("Metabolism"))
gsa = egsea(voom.results=v, contrasts=contrasts,  gs.annots=gs.annots, 
         symbolsMap=v$genes, 
baseGSEAs=egsea.base()[-c(2,5,6,9)], display.top = 5,
          sort.by="avg.rank", egsea.dir="./il13-egsea-report", 
         num.threads = 2, report=FALSE)
topSets(gsa, contrast=1, gs.label="kegg", number = 10)
topSets(gsa, contrast=1, gs.label=1, sort.by="ora", number = 10, 
names.only=FALSE)
topSets(gsa, contrast=0, gs.label="kegg", number = 10)