| weightedGSEA {GIGSEA} | R Documentation |
weightedGSEA performs both SGSEA and MGSEA for a given list of gene sets, and writes out the results.
weightedGSEA(data, geneCol, fcCol, weightCol = NULL,
geneSet = c("MSigDB.KEGG.Pathway", "MSigDB.TF", "MSigDB.miRNA",
"TargetScan.miRNA"), permutationNum = 100, outputDir = getwd(),
MGSEAthres = NULL, verbose = TRUE)
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 |
TRUE
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",
# "TargetScan.miRNA"), permutationNum=10000, outputDir="./GIGSEA" )
# dir("./GIGSEA")