GetCpGsInRegion: Extract probe IDs for CpGs located in a genomic region

In TransBioInfoLab/coMethDMR: Accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies

Extract probe IDs for CpGs located in a genomic region

Description

Extract probe IDs for CpGs located in a genomic region

Usage

GetCpGsInRegion(
  regionName_char,
  region_gr = NULL,
  genome = c("hg19", "hg38"),
  arrayType = c("450k", "EPIC"),
  manifest_gr = NULL,
  ignoreStrand = TRUE
)

Arguments

regionName_char	character string with location information for one region in the format "chrxx:xxxxxx-xxxxxx"
region_gr	An object of class GRanges with location information for one region. If this argument is NULL, then the region in regionName_char is used.
genome	human genome of reference hg19 (default) or hg38
arrayType	Type of array, 450k or EPIC
manifest_gr	A GRanges object with the genome manifest (as returned by ExperimentHub or by ImportSesameData). This function by default ignores this argument in favour of the genome and arrayType arguments.
ignoreStrand	Whether strand can be ignored, default is TRUE

Value

vector of CpG probe IDs mapped to the genomic region

Examples

   
   myRegion_gr <- RegionsToRanges("chr22:18267969-18268249")
   
   GetCpGsInRegion(
     region_gr = myRegion_gr,
     genome = "hg19",
     arrayType = "450k",
     ignoreStrand = TRUE
   )
   

TransBioInfoLab/coMethDMR documentation built on Sept. 14, 2022, 7:09 p.m.