weightedGSEA: weightedGSEA

In zhushijia/GIGSEA: Genotype Imputed Gene Set Enrichment Analysis

Description

weightedGSEA performs both SGSEA and MGSEA for a given list of gene sets, and writes out the results.

Usage

weightedGSEA(data, geneCol, fcCol, weightCol = NULL,
  geneSet = c("MSigDB.KEGG.Pathway", "MSigDB.TF", "MSigDB.miRNA"),
  permutationNum = 100, outputDir = getwd(), MGSEAthres = NULL,
  verbose = TRUE)

Arguments

data	a data frame comprising comlumns: gene names (characer), differential gene expression (numeric) and permuated gene weights (numeric and optional)
geneCol	an integer or a character value indicating the column of gene name
fcCol	an integer or a character value indicating the column of differential gene expression
weightCol	an integer or a character value indicating the column of gene weights
geneSet	a vector of character values indicating the gene sets of interest.
permutationNum	an integer value indicating the number of permutation
outputDir	a character value indicating the directory for saving the results
MGSEAthres	an integer value indicating the thresfold for MGSEA. MGSEA is performed with no more than "MGSEAthres" gene sets
verbose	an boolean value indicating whether or not to print output to the screen

Value

TRUE

Examples

data(heart.metaXcan)
gene <- heart.metaXcan$gene_name
fc <- heart.metaXcan$zscore
usedFrac <- heart.metaXcan$n_snps_used / heart.metaXcan$n_snps_in_cov
r2 <- heart.metaXcan$pred_perf_r2
weights <- usedFrac*r2
data <- data.frame(gene,fc,weights)
# run one-step GIGSEA 
# weightedGSEA(data, geneCol='gene', fcCol='fc', weightCol= 'weights', 
#  geneSet=c("MSigDB.KEGG.Pathway","MSigDB.TF","MSigDB.miRNA") ,
#  permutationNum=10000, outputDir="./GIGSEA" )
# dir("./GIGSEA")

zhushijia/GIGSEA documentation built on May 3, 2019, 10:45 p.m.