gene2set {cogena} | R Documentation |
Generate relationship between genes (gene SYMBOL) and gene-sets, such as Pathway or GO.
gene2set(annofile = NULL, genenames, TermFreq = 0) annotationListToMatrix(annotation, genenames)
annofile |
a gmt file. Examples are from MSigDB Collections. A list of gene set could be find in the vignette of cogena |
genenames |
a SYMBOL gene names charactic vector. |
TermFreq |
a threshold for the Term Frequence. Default is zero. |
annotation |
a value returned by |
an gene and gene-set relationship matrix
data(Psoriasis) #annotaion annoGMT <- "c2.cp.kegg.v5.0.symbols.gmt.xz" annofile <- system.file("extdata", annoGMT, package="cogena") # the DEG gene-sets matrix anno <- gene2set(annofile, rownames(DEexprs))