getTSS: getTSS to fetch GENCODE gene annotation (transcripts level)...

In ELMER: Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

Description

getTSS to fetch GENCODE gene annotation (transcripts level) from Bioconductor package biomaRt If upstream and downstream are specified in TSS list, promoter regions of GENCODE gene will be generated.

Usage

getTSS(genome = "hg38", TSS = list(upstream = NULL, downstream = NULL))

Arguments

genome	Which genome build will be used: hg38 (default) or hg19.
TSS	A list. Contains upstream and downstream like TSS=list(upstream, downstream). When upstream and downstream is specified, coordinates of promoter regions with gene annotation will be generated.

Value

GENCODE gene annotation if TSS is not specified. Coordinates of GENCODE gene promoter regions if TSS is specified.

Author(s)

Lijing Yao (maintainer: [e-mail])

Examples

# get GENCODE gene annotation (transcripts level)
## Not run: 
    getTSS <- getTSS()
    getTSS <- getTSS(genome.build = "hg38", TSS=list(upstream=1000, downstream=1000))

## End(Not run)

ELMER documentation built on Nov. 8, 2020, 4:59 p.m.