nullDist: Null distribution

In CMPG/signet: signet: Selection Inference in Gene NETworks

Null distribution

Description

Generate the high-scores null distribution to compute empirical p-values for each biological pathway.

Usage

nullDist(pathways, scores, n = 1000, background)

Arguments

pathways	A list of graphNEL objects.
scores	A data frame in which the first column corresponds to the gene ID and the second column contains the gene scores.
n	Number of null high-scores to compute (default = 1000).
background	Optional. Background distribution computed using the ⁠backgroundDist⁠ function.

Value

A vector of subnetworks scores obtained under the null hypothesis. Must be used as input of the ⁠testSubnet⁠ function.

Examples

# Get KEGG pathways from the package graphite:
# library(graphite)
# kegg <- pathways("hsapiens", "kegg")
# kegg_human <- lapply(kegg, pathwayGraph)

data(daub13) # load the gene scores

# generate the null distribution (here, only 5 values, but
# at least 1000 are advised)
null <- nullDist(kegg_human, scores, n = 5)

CMPG/signet documentation built on Jan. 31, 2024, 12:56 a.m.