rankedGSEA: PCA-based Gene Set Enrichment Analysis (GSEA)

In sidiropoulos/PSigA: A gene-signature ranking method based on sample density in PCA space

Description

...

Usage

rankedGSEA(data, signatures, p.adj = p.adjust.methods, pcs = c(1, 2),
  filtered = FALSE)

Arguments

data	Gene expression matrix where rownames correspond to unique gene identifiers in signature format and columns correspond to samples.
signatures	list where every entry is a character vector of the gene names that correspond to a gene-pathway. If the gene format is different from the one in rownames(data), use parseData first.
p.adj	p-value correction method. See p.adjust.
pcs	principal components to perform GSEA on. Default: c(1,2).
filtered	logical value indicating if genes in the supplied signature list that are not present in the data have been filtered out. Default: FALSE.

sidiropoulos/PSigA documentation built on May 29, 2019, 9:58 p.m.