mbrAssociation-methods: Motifs analysis and inference of 'dual regulons'.

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

Description

This function takes an MBR object and compares the shared regulon targets in order to test whether regulon pairs agree on the predicted downstream effects.

Usage

## S4 method for signature 'MBR'
mbrAssociation(object, regulatoryElements1 = NULL,
  regulatoryElements2 = NULL, minRegulonSize = 30, prob = 0.95,
  estimator = "spearman", pAdjustMethod = "BH", verbose = TRUE)

Arguments

object	A processed object of class MBR evaluated by the methods mbrPermutation, mbrBootstrap and mbrDpiFilter.
regulatoryElements1	An optional character vector specifying which 'TNI1' regulatory elements should be evaluated. If 'NULL' all regulatory elements will be evaluated.
regulatoryElements2	An optional character vector specifying which 'TNI2' regulatory elements should be evaluated. If 'NULL' all regulatory elements will be evaluated.
minRegulonSize	A single integer or numeric value specifying the minimum number of elements in a regulon. Gene sets with fewer than this number are removed from the analysis.
prob	A quantile filter applyed to the association metric used to infer 'dual regulons'.
estimator	A character value specifying the estimator used in the association analysis. One of "spearman" (default), "kendall", or "pearson", can be abbreviated.
pAdjustMethod	A single character value specifying the p-value adjustment method to be used (see 'p.adjust' for details).
verbose	A single logical value specifying to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE).

Value

An MBR object with two data.frames in the slot 'results' listing the inferred 'dual regulons' and a hypergeometric test for each 'dual regulon'.

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)

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