mbrPermutation-methods: Inference of transcriptional networks.

In chagasVinicius/RTNmotifs: analysis of co-regulatory network motifs and inference of 'dual regulons'.

Description

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

Usage

## 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

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 13, 2019, 3:10 p.m.