lift: Lift Over Genome Build

In tpq/miSciTools: Miscellaneous Science Tools for Bioinformatic Analysis

Description

This function simplifies the process of "lifting over" coordinates from one genome build to another by automatically downloading the necessary .over.chain.gz file.

Usage

lift(object, from = "hg18", to = "hg19", flatGrl = TRUE)

Arguments

object	A GRanges object.
from	A character string. The initial UCSC equivalent genome build (e.g., hg18).
to	A character string. The target UCSC equivalent genome build (e.g., hg19).
flatGrl	A logical scalar. Toggles whether to collapse the default GRangesList output to a GRanges output.

Details

This function will convert any non-UCSC coordinates to UCSC equivalents. Make sure the arguments from and to refer to valid UCSC genome builds. Feature names will get lost during 'lift over'. To retain, these labels, consider storing names as a separate column in the GRanges object.

Value

A GRangesList object or GRanges object.

tpq/miSciTools documentation built on Sept. 16, 2019, 4:43 p.m.