getTSS {TCGAbiolinks} | R Documentation

## 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 = "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.

### 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)

[Package TCGAbiolinks version 2.10.5 Index]