pathwaysplice: pathwaysplice

In aiminy/PathwaySplice: An R Package for Adjusting Bias in Gene Set Enrichment Analysis

Description

This function computes p-values for each gene set and output the list of differentially expressed genes within the gene set. The user can select serveral statistical methods for computing p-values

Usage

pathwaysplice(pwf, genome, id, gene.model, gene2cat = NULL,
  test.cats = c("GO:CC", "GO:BP", "GO:MF"), method = "Wallenius",
  repcnt = 2000, use_genes_without_cat = FALSE)

Arguments

pwf	probability weight function
genome	genome you will use
id	which gene id
gene.model	which gene model
gene2cat	a list with gene as name and category as value
test.cats	the category you choose
method	which method for calculting overpresentation p-value
repcnt	the number of replications
use_genes_without_cat	whether using genes without category or not

Value

The gene set enrichment results for gene sets

aiminy/PathwaySplice documentation built on May 10, 2019, 7:38 a.m.