nullDist: Null distribution

Description Usage Arguments Value Examples

View source: R/nullDist.R

Description

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

Usage

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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

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# 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 Nov. 24, 2018, 8:03 p.m.