tna.synergy {RTN}R Documentation

Synergy analysis over a list of regulons (deprecated function).

Description

This function is provided for compatibility with older versions of ‘RTN’ only, and will be defunct at the next release (see details).

Usage

tna.synergy(object, pValueCutoff=0.05, pAdjustMethod="BH", minRegulonSize=15, minIntersectSize=1,
                  nPermutations=1000, exponent=1, tnet="ref", orderAbsValue=TRUE, stepFilter=TRUE,
                  tfs=NULL, verbose=TRUE)

Arguments

object

a preprocessed object of class 'TNA' TNA-class.

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' for details).

minRegulonSize

a single integer or numeric value specifying the minimum number of elements in a regulon that must map to elements of the gene universe. Gene sets with fewer than this number are removed from the analysis.

minIntersectSize

a single integer or numeric value specifying the minimum number of elements in the intersect between any two regulons in the synergy analysis (as percentage value).

nPermutations

a single integer or numeric value specifying the number of permutations for deriving p-values in GSEA.

exponent

a single integer or numeric value used in weighting phenotypes in GSEA (see 'gseaScores' function at HTSanalyzeR).

tnet

a single character value specifying which transcriptional network should to used to compute the synergy and shadow analyses. Options: "dpi" and "ref".

orderAbsValue

a single logical value indicating whether the values should be converted to absolute values and then ordered (if TRUE), or ordered as they are (if FALSE).

stepFilter

a single logical value specifying to use a step-filter algorithm removing non-significant regulons derived from tna.gsea1 (when stepFilter=TRUE) or not (when stepFilter=FALSE). It may have a substantial impact on the overall processing time.

tfs

an optional vector with transcription factor identifiers (this option overrides the 'stepFilter' argument).

verbose

a single logical value specifying to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE).

Details

The 'tna.synergy' function is deprecated and will be made defunct. For pairwise regulon analysis, please consider using the 'RTNduals' package.

Value

a data frame in the slot "results".


[Package RTN version 2.10.1 Index]