alignToTSS {VplotR} | R Documentation

## 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)

[Package VplotR version 1.0.0 Index]