alignToTSS: A function to re-align a GRanges object to TSSs

In js2264/VplotR: Set of tools to make V-plots and compute footprint profiles

A function to re-align a GRanges object to TSSs

Description

This function re-aligns ranges (typically regulatory elements) to a set of coordinates, either the TSS column or the TSS.fwd and TSS.rev columns. If none are found, the function assumes the ranges are promoters and that the end or the ranges are the TSSs.

Usage

alignToTSS(granges, upstream = 0, downstream = 1)

Arguments

granges	A stranded GRanges object with a TSS column or TSS.rev and TSS.fwd columns
upstream	How many bases upstream of the TSS should the GRanges object by extended by? [Default: 0]
downstream	How many bases downstream of the TSS should the GRanges object by extended by? [Default: 1]

Value

GRanges aligned to the TSS column or to TSS.rev and TSS.fwd columns, and extended by upstream/downstream bp.

Examples

data(ce11_proms)
ce11_proms
alignToTSS(ce11_proms)

js2264/VplotR documentation built on Jan. 4, 2024, 7:49 p.m.