gset {gsEasy}

Gene set enrichment test

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)