allezTable: Extract a table of top-ranked functional sets from allez...

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

Description

Thresholds allez setscores element by number of genes in the set and z-score; orders sets from highest to lowest set mean. A functional set is removed if it contains the entire set of input gene scores.

Usage

allezTable(allez.out, n.low = 5, n.upp = 500, n.cell=0, zthr = 5, symbol = FALSE, in.set = FALSE)

Arguments

allez.out	list object, output from allez function
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 for binary scores
zthr	numeric, threshold z-scores at this level
symbol	logical; if TRUE, list gene symbols in set, otherwise list gene or probe ID
in.set	logical; if TRUE, will list genes in set that had scores > 0

Value

A subset of allez.out$setscores, thresholded by z-score and number of genes in a set, ordered by set.means. genes column is ordered by gene scores.

Author(s)

Aimee Teo Broman and Michael Newton

See Also

allez

Examples

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

allezTable(npc.kegg,symbol=TRUE)

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