mbrAssociation,MBR-method {RTNduals} | R Documentation |
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.
## S4 method for signature 'MBR' mbrAssociation(object, regulatoryElements = NULL, minRegulonSize = 15, doSizeFilter = FALSE, pValueCutoff = 0.001, pAdjustMethod = "bonferroni", estimator = "spearman", nPermutations = 1000, miFilter = TRUE, verbose = TRUE)
object |
A processed object of class MBR |
regulatoryElements |
An optional character vector specifying which 'TNI' 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. |
doSizeFilter |
a logical value. If TRUE, negative and positive targets are independently verified by the 'minRegulonSize' argument. |
pValueCutoff |
a single numeric value specifying the cutoff for p-values considered significant. |
pAdjustMethod |
A single character value specifying the p-value adjustment method to be used (see 'p.adjust' function for details). |
estimator |
A character value specifying the estimator used in the association analysis. One of "spearman" (default), "kendall", or "pearson". |
nPermutations |
A single integer value specifying the number of permutations for deriving p-values associating regulon pairs. |
miFilter |
A single logical value specifying to apply the 'miFilter' between two regulators. |
verbose |
A single logical value specifying to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE). |
An MBR object with two data.frames in the slot 'results' listing the inferred 'dual regulons' and correspoding statistics.
##--- load a dataset for demonstration data("tniData", package = "RTN") gexp <- tniData$expData annot <- tniData$rowAnnotation tfs <- c("IRF8","IRF1","PRDM1","E2F3","STAT4","LMO4","ZNF552") ##--- construct a tni object rtni <- tni.constructor(gexp, regulatoryElements = tfs, rowAnnotation=annot) ##--- compute regulons ## set nPermutations>=1000 rtni <- tni.permutation(rtni, nPermutations=30) ## set nBootstrap>=100 rtni <- tni.bootstrap(rtni, nBootstrap=30) ## 'eps=NA' estimates threshold from empirical null rtni <- tni.dpi.filter(rtni, eps=NA) ##--- construct a mbr object rmbr <- tni2mbrPreprocess(rtni) ##--- run mbrAssociation ## set nPermutations>=1000 rmbr <- mbrAssociation(rmbr, pValueCutoff = 0.05, nPermutations=30)