change_genomic_coordinate: change the genomic coordinate system of inputRegion by...

In geneprophet/BSDMR: a region-based method for quantitating the conservation and divergence of methylation patterns between species by high order features

Description

change the genomic coordinate system of inputRegion by liftOver with chainFile

Usage

change_genomic_coordinate(
  inputRegion,
  chainFile,
  targetAnnotation = NULL,
  is_parallel = TRUE,
  no_cores = NULL
)

Arguments

inputRegion	the region you want to change the genomic coordinate system,a GRanges object. Generally, the inputRegin is a result of cluster_sites_to_region.
chainFile	a chainFile of liftOver. for example, if you want mapping the the inputRegion from hg38 to mm10, then the chainFile must be "hg38ToMm10.over.chain". you can download from the source <http://hgdownload.soe.ucsc.edu/downloads.html#liftover>
targetAnnotation	the GRanges object to annotate the result of liftOver, a GRanges object. Generally, the targetAnnotation is a result of read_annotation. default value is null.
is_parallel	Logical, indicating if code should be run in parallel.
no_cores	if you have specify the is_parallel is ture ,you can specify the number of parallel cores

Value

A GRanges object corrsponding to the inputRegion in another genomic coordinate system

Author(s)

Hongen Kang [e-mail]

Examples

 
## Not run: 
filePath <- system.file("extdata", "hg38ToMm10.over.chain", package = "BSDMR")
mouse_region <- change_genomic_coordinate(human_region,filePath,mouse_anno)

## End(Not run)

geneprophet/BSDMR documentation built on March 3, 2021, 5:50 a.m.