topTraitsOfTargets {TFutils}R Documentation

Use MSigDB TF targets resource to find targets of input TF and find traits to which these targets have been mapped

Description

Use MSigDB TF targets resource to find targets of input TF and find traits to which these targets have been mapped

Usage

topTraitsOfTargets(TFsym, gsc, gwcat, ntraits = 6, force = FALSE, ...)

Arguments

TFsym

character(1) symbol for a TF must be present in tftCollMap[, "hgnc.heur"]

gsc

an instance of GeneSetCollection-class, intended to enumerate targets of a single transcription factor in each GeneSet, as in TFutils::tftColl

gwcat

instance of gwaswloc-class

ntraits

numeric(1) number of traits to report

force

logical see note, set to true if you want to skip mapping from TFsym to a specific motif or TF identifier used as name of a GeneSet in gsc

...

character() vector of fields in mcols(gwcat) to include

Note

If tftCollMap[, "hgnc.heur"] does not possess the necessary symbol, set force = TRUE to use a known 'motif' name among names(gsc)

Examples

suppressPackageStartupMessages({
library(GSEABase)
library(TFutils)
})  # more results if you substitute ebicat37 from gwascat below
topTraitsOfTargets("MTF1" , tftColl, gwascat_hg19_chr17)

[Package TFutils version 1.4.0 Index]