gscEntrez: Create a GeneSetCollection from probe annotations using...

In peterjuv/FunGenPipe: Tools for building function genomics pipelines

Description

Create a GeneSetCollection from probe annotations using ENTREZID

Usage

gscKeggEntrez(annPrb, idName = "PROBEID", organism = "mmu")

gscTransfacEntrez(
  annPrb,
  idName = "PROBEID",
  fac2drDF,
  by = "factor.FA",
  annTransfac
)

Arguments

annPrb	Data frame probe annotations for mapping ENTREZID -> PROBEID; ENTREZIDs may be collapsed using ";"
idName	Character column name from annPrb that represents IDs of probes which are used for mapping paths to a vector of probes; default "PROBEID"
organism	Character KEGG organism 3-letter code, e.g. "mmu", "hsa", etc.
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"
annTransfac	Data frame TRANSFAC annotations from getAnnTransfacEntrez()

Value

GeneSetCollection

Functions

• gscKeggEntrez: Create a KEGG GeneSetCollection from probe annotations using ENTREZID using KEGG organism 3-letter code

• gscTransfacEntrez: Create a TRANSFAC GeneSetCollection from probe annotations using ENTREZID

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