nullDist: Null distribution

In signet: signet: Selection Inference in Gene NETworks

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)

signet documentation built on April 28, 2020, 7:54 p.m.