tna.overlap {RTN} | R Documentation |
This function is provided for compatibility with older versions of ‘RTN’ only, and will be defunct at the next release (see details).
tna.overlap(object, pValueCutoff=0.05, pAdjustMethod="BH", minRegulonSize=15, tnet="ref", tfs=NULL, verbose=TRUE)
object |
a preprocessed object of class 'TNA' |
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. |
tnet |
a single character value specifying which transcriptional network should to used to compute the overlap analysis. Options: "dpi" and "ref". |
tfs |
an optional vector with transcription factor identifiers. |
verbose |
a single logical value specifying to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE). |
The 'tna.overlap' function is deprecated and will be made defunct. For pairwise regulon analysis, please consider using the 'RTNduals' package.
a data frame in the slot "results".