topTraitsOfTargets: Use MSigDB TF targets resource to find targets of input TF...

Description Usage Arguments Note Examples

View source: R/genepi.R

Description

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

Usage

1
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

1
2
3
4
5
suppressPackageStartupMessages({
library(GSEABase)
library(TFutils)
})  # more results if you substitute ebicat37 from gwascat below
topTraitsOfTargets("MTF1" , tftColl, gwascat_hg19_chr17)

TFutils documentation built on May 2, 2020, 2:01 a.m.