mbrDuals-methods: A summary for results from the MBR methods.

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

Description

This function lists the inferred 'dual regulons' and, if available, adds external evidences.

Usage

## S4 method for signature 'MBR'
mbrDuals(object, supplementary.table = NULL,
  evidenceColname = NULL, verbose = TRUE)

Arguments

object	A processed object of class MBR evaluated by the method mbrAssociation.
supplementary.table	An optional 'data.frame' with three columns representing (1) regulatory elements of 'TNI1', (2) regulatory elements of 'TNI2', and (3) external evidences between the regulatory elements.
evidenceColname	A single character value specifying a column in the 'supplementary.table'.
verbose	A single logical value specifying to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE).

Value

An MBR object with a data.frame in the slot 'results' listing the input additional evidences.

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)
##---mbrDpiFilter
rmbr <- mbrDpiFilter(rmbr)
##---mbrAssociation
rmbr <- mbrAssociation(rmbr, prob=0.75)
##---a 'toy' table with supplementary evidences
motifsInformation <- mbrGet(rmbr, what="motifsInformation")
n <- nrow(motifsInformation)
supplementaryTable <- motifsInformation[1:n,c("Regulon1","Regulon2")]
supplementaryTable$ToyEvidence <- rnorm(n)
##---mbrDuals
rmbr <- mbrDuals(rmbr, supplementary.table = supplementaryTable, 
evidenceColname = "ToyEvidence")
##---motifsInformation with 'Evidence'
motifsInformation <- mbrGet(rmbr, what="motifsInformation")
head(motifsInformation)

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