mbrPermutation-methods: Inference of transcriptional networks.

Description Usage Arguments Value Examples

Description

This function takes an MBR object and computes two transcriptional networks inferred by mutual information (with multiple hypothesis testing corrections).

Usage

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## S4 method for signature 'MBR'
mbrPermutation(object, verbose = TRUE, ...)

Arguments

object

A preprocessed object of class MBR.

verbose

A single logical value specifying to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE).

...

Additional arguments passed on to the tni.permutation function.

Value

An MBR object with two mutual information matrices, one in each "TNI" slot.

Examples

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data("dt4rtn", package = "RTN")
gexp <- dt4rtn$gexp
annot <- dt4rtn$gexpIDs
tfs1 <- dt4rtn$tfs[c("IRF8","IRF1","PRDM1","AFF3","E2F3")]
tfs2 <- dt4rtn$tfs[c("HCLS1","STAT4","STAT1","LMO4","ZNF552")]
##---mbrPreprocess
rmbr <- mbrPreprocess(gexp=gexp, regulatoryElements1 = tfs1, 
regulatoryElements2=tfs2, gexpIDs=annot)
##---mbrPermutation
rmbr <- mbrPermutation(rmbr, nPermutations=10)

chagasVinicius/RTNmotifs documentation built on May 12, 2017, 2:15 a.m.