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

In BioinformaticsFMRP/TCGAbiolinks: TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

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.

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 = c("hg38", "hg19"),
  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.

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)

BioinformaticsFMRP/TCGAbiolinks documentation built on April 12, 2024, 2:08 a.m.