condorCoreEnrich: Compare qscore distribution of a subset of nodes to all other...

In netZoo/netZooR: Unified methods for the inference and analysis of gene regulatory networks

Compare qscore distribution of a subset of nodes to all other nodes.

Description

Compute one-sided KS and wilcox tests to determine if a subset of nodes has a stochastically larger qscore distribution.

Usage

condorCoreEnrich(test_nodes, q, perm = FALSE, plot.hist = FALSE, nsamp = 1000)

Arguments

test_nodes	is a list containing the subset of nodes (of one node class –blue or red–only) to be tested
q	is a two column data frame containing the node names in the first column and the q-scores in the second column.
perm	if TRUE, run permutation tests. Else, run ks.test and wilcox.test only.
plot.hist	if TRUE, produces two histograms of test statistics from permutation tests, one for KS and one for wilcoxon and a red dot for true labeling. Only works if perm=TRUE.
nsamp	Number of permutation tests to run

Value

if perm=FALSE, the analytical p-values from ks.test and wilcox.test

if perm=TRUE, the permutation p-values are provided in addition to the analytical values.

Note

ks.test and wilcox.test will throw warnings due to the presence of ties, so the p-values will be approximate. See those functions for further details.

Examples

r = c(1,1,1,2,2,2,3,3,3,4,4);
b = c(1,2,3,1,2,4,2,3,4,3,4);
reds <- c("Alice","Sue","Janine","Mary")
blues <- c("Bob","John","Ed","Hank")
elist <- data.frame(red=reds[r],blue=blues[b])
condor.object <- createCondorObject(elist)
condor.object <- condorCluster(condor.object)
condor.object <- condorQscore(condor.object) 
q_in <- condor.object$qscores$red.qscore
out <- condorCoreEnrich(c("Alice","Mary"),q=q_in,perm=TRUE,plot.hist=TRUE)

netZoo/netZooR documentation built on Oct. 16, 2024, 10:23 p.m.