getAnnTransfacEntrez: Get annotations for PGSEA from TRANSFAC using factor names...
In peterjuv/FunGenPipe: Tools for building function genomics pipelines

Description Usage Arguments Details Value

Import TRANSFAC data frame fac2drDF and filter using ENTREZID(s) (may be collapsed by ";") from an ExpressionSet eset. 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

getAnnTransfacEntrez(
  fac2drDF,
  by = "factor.FA",
  eset = NULL,
  patternExcludeFactor = NULL,
  addURL = FALSE
)

`fac2drDF`	Data frame TRANSFAC database
`by`	Character column name from `fac2drDF` that is used to collapse anotations by; must start with "factor.", default "factor.FA"; annotations are not collapsed if equal to "factor.AC", but column names of the output are still in plural, e.g. "factorFAs"
`eset`	Expression set with anotations ENTREZID(s) (my be collapsed by ";") within fData(); these are used only to limit TFs to ENTREZIDs; default NULL
`patternExcludeFactor`	Regular expression pattern for exclusion of TFs based on column `by`; default NULL"
`addURL`	Logical add a column with factor URL (factorURL), default FALSE

Warning: annotations are unique and individually sorted; thus, they are not matched by their position within the collapsed strings. Warning: Factor URLs will only be accessible from IPs that are licensed with QIAGEN portal https://apps.ingenuity.com/ingsso/. Old TODO: consider creating new factors for fac2drDF_entrez_sym or even more general, e.g. using fac2drDF or or fac2drDF_osXX.

A data frame with collapsed annotations including factor accessions (factorACs) and names (factorFAs), site accessions (siteACs), gene accessions (geneACs) and short gene terms/symbols (geneSDs), and optional factor URLs (factorURLs)

peterjuv/FunGenPipe documentation built on June 18, 2021, 3:38 a.m.