addSingleGeneSets {gep2pep} | R Documentation |
This function can be used to add single-gene (as opposed to pathway) -based collections. Sets including a single gene don't need to go through normal Kolmogorov-Smirnov statistic computation and are treated differently for performance.
addSingleGeneSets(rp, genes, organism = "Homo Sapiens")
rp |
A repository created by |
genes |
a character vector containing the gene names. For each
og them a single-gene |
organism |
Character vector used to annotate the created sets. "Homo Sapiens" by default. |
Enrichment Scores and p-values for sets including a single gene are
computed with dedicated (fast) routines. Although a statistic based
on a single gene is not efficient per se, it is useful to have data
in the same format as pathway-based profiles. buildPEPs
internally calls single gene dedicated routines whenever a gene set
collection is tagged (see repo function tag
) with "SGE"
("Single Gene Expression"), which is done automatically by
addSingleGeneSets
. In that case, the min_size
parameter is ignored.
Nothing, used for side effects.
buildPEPs
db <- loadSamplePWS() repo_path <- file.path(tempdir(), "gep2pepTemp") rp <- createRepository(repo_path, db) ## The following will create PEPs in 2 separate files geps <- loadSampleGEP() addSingleGeneSets(rp, rownames(geps)) unlink(repo_path, TRUE)