grabTab: create table of TF targets and related metadata

In vjcitn/TFutils: TFutils

Description

create table of TF targets and related metadata

Usage

grabTab(
  tfstub = "STAT1",
  gscoll = TFutils::tftColl,
  orgdb = org.Hs.eg.db::org.Hs.eg.db,
  gwrngs = TFutils::gwascat_hg19_chr17
)

Arguments

tfstub	character(1) gene-like symbol for TF; will be grepped in names(gscoll)
gscoll	a GSEABase GeneSetCollection
orgdb	an instance of OrgDb as defined in AnnotationDbi
gwrngs	a GRanges representing EBI gwascat, must have DISEASE/TRAIT, MAPPED_GENE

Value

data.frame instance

Note

This function will link together information on targets of a given TF to the GWAS catalog.

Examples

gt = grabTab("VDR", gscoll=TFutils::tftColl,
   orgdb=org.Hs.eg.db::org.Hs.eg.db, gwrngs=TFutils::gwascat_hg19_chr17)
dim(gt)
head(gt)

vjcitn/TFutils documentation built on Oct. 25, 2021, 3:01 p.m.