grabTab: create table of TF targets and related metadata

Description Usage Arguments Value Note Examples

View source: R/grabTab.R

Description

create table of TF targets and related metadata

Usage

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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

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

shwetagopaul92/TFutils documentation built on April 20, 2018, 7:57 a.m.