getTSS: get TSS file for use in combineAnnotatePeaks function. The...

In Mathelab/ALTRE: Workflow for Identifying Regulatory Elements from Chromatin Accessibility Assay Data

Description

get TSS file for use in combineAnnotatePeaks function. The default functionality (with no parameters suppplied) is to retrieve human TSS from ensembldb annotation 75, which is hg19. If this isn't suitable for your organism or human genome alignment you will need to supply your own text file with TSS information. The first three columns must contain the chr start and stop coordinates, and 4th column must contain the gene name.

Usage

getTSS(file = NULL)

Arguments

file	filname of TSS for organism under study

Examples

## Not run: 
TSSannot <- getTSS(file="./gtfManipulation/Homo_sapiens.GRCh37.75_exon1only.bed")

## End(Not run)

Mathelab/ALTRE documentation built on May 7, 2019, 3:41 p.m.