generate.ora.data: Over-Representation Analysis.

In vittoriofortino84/ThETA: Transcriptome-based efficacy estimates of target(gene)-disease associations

Description

It compiles the over-representation analysis for each gene set in the input list.

Usage

generate.ora.data(
  input,
  databases = c("GO", "KEGG"),
  orgdb_go = "org.Hs.eg.db",
  orgdb_kegg = "hsa",
  apval = 0.01,
  verbose = TRUE
)

Arguments

input	a list of charcater vectors representing gene sets.
databases	character vector indicating the biological annotations to be used for the ORA. Possible values are: GO, KEGG and REACTOME enrichment functions.
orgdb_go	a character specifying the organism for GO. Deafault value is org.Hs.eg.db.
orgdb_kegg	a character specifying the organism for KEGG. Deafault value is hsa.
apval	a number indicating the cutoff for the adjusted pvalue.
verbose	logical indicating whether the messages will be displayed or not in the screen.

Value

a list or ORA results.

vittoriofortino84/ThETA documentation built on May 23, 2021, 4:24 a.m.