annTFbyFA: Depricated: Get annotations for PGSEA from TRANSFAC using...
In peterjuv/FunGenPipe: Tools for building function genomics pipelines

Description Usage Arguments Value

Import TRANSFAC data.frame fac2drDF and filter using ENTREZIDs (may be collapsed by ";") from an ExpressionSet. Data frame includes columns: factor.AC site.AC factor.BSq gene.AC gene.DRac2 gene.DRdbName2 factorURL factor.FA gene.SD gene.DE TFs may be excluded based on a pattern matching their names, for example: "[^(hsa)]-miR" will exclude non-human microRNAs "(-miR)|(isoform)" will exclude all microRNAs and isoforms Old TODO: consider creating new factors for fac2drDF_entrez_sym or even more general, e.g. using fac2drDF or or fac2drDF_osXX

1	annTFbyFA(fac2drDF, eset = NULL, patternExcludeFactorFA = NULL)

`fac2drDF`	Data frame transcription factor
`eset`	Expression set with anotations ENTREZID within fData(); these are used to limit TFs to ENTREZIDs; default NULL
`patternExcludeFactorFA`	Regular expression pattern for exclusion of TFs based on their names (i.e., factor.FA); default NULL;