txs: txs to fetch USCS gene annotation (transcripts level) from...

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

Description

txs is a function to fetch USCS gene annotation (transcripts level) from Bioconductor package Homo.sapians. If upstream and downstream are specified in TSS list, promoter regions of USCS gene will be generated.

Usage

txs(TSS = list(upstream = NULL, downstream = NULL))

Arguments

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

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

Author(s)

Lijing Yao (maintainer: [e-mail])

Examples

# get UCSC gene annotation (transcripts level)
txs <- txs()
# get coordinate of all UCSC promoter regions +/-1000bp of TSSs
## Not run: 
txs <- txs(TSS=list(upstream=1000, downstream=1000))

## End(Not run)

lijingya/ELMER documentation built on May 21, 2019, 6:14 a.m.