easyLift

R package for easy mm9 <-> mm10 / hg19 <-> hg38

Install

devtools::install_github("caleblareau/easyLift")

Quick Usage

Grab the convenient Rscript from the vignettes folder to run everything from the command line like so–

lareauc$ Rscript easyLiftOver.R randPeaks.bed hg19_hg38
[1] "Attempted to write to file: randPeaks.bedover"

• First parameter is the .bed file that one wants to lift over.
• Second parameter is the liftover chain specification. The coding is {FROM}_{TO}.
• Third (optional) parameter is the output file name. If no file is supplied, then “over” will be appened to the .bed file supplied in the first argument.

Support

For the second (map) parameter, we currently support any one of:

• mm9_mm10
• mm10_mm9
• hg19_hg38
• hg38_hg19

For the first (from) parameter, the file extension doesn’t necessarily need to be .bed but just resemble a .bed (e.g. .narrowPeak

Advanced Usage

• In the R environment, using easyLift::easyLiftOver on a GRanges object will return a GRanges object with lifted over coordinates again specified by the second (map) parameter.

• If you have a .chain file that you want to use (e.g. for going from mm10 to hg38), specify that file path in the second argument. This gives a sample URL structure to access these cross-species chain files from UCSC.

http://hgdownload.cse.ucsc.edu/goldenpath/hg38/vsMm10/