liftover_CpGs: Converts from one reference to another via...

In CompEpigen/scMethrix: Fast and efficient summarization of single cell whole genome bisulfate data

Description

Converts from one reference to another via rtracklayer::liftOver

Usage

liftover_CpGs(scm, chain = NULL, target_genome = NULL, verbose = TRUE)

Arguments

scm	scMethrix; the single cell methylation experiment
chain	string; the file location for the desired chain to use in liftOver
target_genome	string; the target genome. This will be update the genome field in the output scMethrix object
verbose	boolean; Flag for outputting function status messages. Default = TRUE

Details

This conversion is one-to-many, so for consistency, only the first element in the target assembly is used.

LiftOver chains can be found here: UCSC

Here's links to common chains: http://hgdownload.cse.ucsc.edu/goldenpath/hg38/liftOver/hg38ToHg19.over.chain.gzhg38 to hg19 https://hgdownload.soe.ucsc.edu/gbdb/hg19/liftOver/hg19ToHg38.over.chain.gzhg19 to hg38

Value

a list of data.table containing number of CpG's and contig lengths

Examples

## Not run: 
hg19_cpgs = methrix::extract_CPGs(ref_genome = 'BSgenome.Hsapiens.UCSC.hg19')

## End(Not run)

CompEpigen/scMethrix documentation built on Nov. 6, 2021, 3:09 p.m.