tna.shadow {RTN} | R Documentation

## shadow 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.shadow(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 shadow 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 shadow 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.shadow 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]