msigdb_gsea {GenomicSuperSignature} | R Documentation |
MSigDB GSEA results
msigdb_gsea( ind, RAVmodel, category = "C2", n = NULL, pvalueCutoff = 0.5, minGSSize = 10, maxGSSize = 500, pAdjustMethod = "BH", verbose = FALSE, seed = FALSE, by = "fgsea", geneSets = NULL )
ind |
An interger. Index of RAV to apply GSEA. |
RAVmodel |
PCAGenomicSignature object. |
category |
A character vector representing MSigDB category. Options are "H", "C1", "C2"(default), "C3", "C4", "C5", "C6", and "C7" |
n |
An interger. The number of top and bottom enriched pathways to plot.
Default is |
pvalueCutoff |
Cutoff for both pvalue and p.adjust. Default is 0.5. |
minGSSize |
A mininum size of gene set to be analyzed |
maxGSSize |
A maximum size of gene set to be analyzed |
pAdjustMethod |
p-value adjustment methods, which will be used as an
input for |
verbose |
Logical. Default is FALSE. |
seed |
Logical. Default is FALSE. |
by |
Available options are |
geneSets |
Custom genesets to use with MSigDB genesets. It should be in a named list format. |
Barplot of GSEA output. Top and bottom n
genesets based on NES
are plotted and qvalues are denoted by color.