gset: Gene set enrichment test

In gsEasy: Gene Set Enrichment Analysis in R

Description

Gene set enrichment test

Usage

gset(S, N = NULL, r = NULL, p = 1, min_its = 200, max_its = 1e+05,
  significance_threshold = 0.05, log_dismiss = -10, raw_score = FALSE)

Arguments

S	Ranks of gene set
N	Integer value. Only required if r is not specified.
r	Rank/correlation scores. If S is character, then r must be named by gene or be a character vector of the gene names in rank order (necessarily containing S).
p	Weighting of ranking/correlations, see Subramanian et. al 2005.
min_its	Minimum number of null permutations to compare.
max_its	Maximum number of null permutations to compare.
significance_threshold	Maximum p-value of significant result.
log_dismiss	Threshold log probability of returning a significant result, below which function returns current p-value.
raw_score	Logical value determining whether to return the raw value of the gene set enrichment score.

Value

Numeric value - p-value of enrichment.

Examples

gset(S=1:5 * 2, N=1000)
gset(S=letters[1:3], r=letters)

Example output

[1] 9.9999e-06
[1] 0.0003099969

gsEasy documentation built on May 27, 2021, 1:06 a.m.