allezMat: Creates an indicator matrix of functional sets vs. genes

In atbroman/allez: Random-set calibration of gene-set statistics

Description

Given output list from allez, this function will create an indicator matrix of the highest ranking sets; sets IDs are listed as columns, genes as rows.

Usage

allezMat(allez.out, n.low = 5, n.upp = 500, n.cell = 0, zthr = 3)

Arguments

allez.out	list output from allez
n.low	numeric, smallest number of genes in a set to consider for ranking
n.upp	numeric, largest number of genes in a set to consider for ranking
n.cell	numeric, minimum number of genes in a set with score>0, mainly used in conjunction with binary scores
zthr	numeric, keep sets with z-scores at this level or higher

Value

A matrix of 0,1, with genes listed as rows and sets as columns; matrix element is a 0 if the gene is not in the set, and 1 if the gene is part of the set.

Author(s)

Aimee Teo Broman and Michael Newton

Examples

data(npc)
scores  <- (1/2)*sqrt(28)*log((1-npc)/(1+npc))
npc.kegg <- allez(scores, lib="hgu133plus2", sets="KEGG")

amat <- allezMat(npc.kegg,zthr=5)
head(amat)

atbroman/allez documentation built on May 10, 2019, 2:08 p.m.