tni2mbrPreprocess-methods: A preprocessing function for objects of class MBR.

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

Description

This function merges two TNI class objects and creates one MBR class object.

Usage

## S4 method for signature 'TNI'
tni2mbrPreprocess(tni1, tni2, verbose = TRUE)

Arguments

tni1	A 'TNI' class object.
tni2	Another 'TNI' class object
verbose	A single logical value specifying to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE).

Value

An MBR object.

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)
##---mbrBootstrap
rmbr <- mbrBootstrap(rmbr, nBootstrap=10)
rmbr <- mbrDpiFilter(rmbr)
##---tni2mbrPreprocess
tni1 <- mbrGet(rmbr, what="TNI1")
tni2 <- mbrGet(rmbr, what="TNI2")
rmbr <- tni2mbrPreprocess(tni1, tni2)

chagasVinicius/RTNduals-alpha documentation built on May 13, 2019, 3:10 p.m.