Extract probe IDs for CpGs located in a genomic region

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
   )
#> snapshotDate(): 2021-05-18
#> see ?sesameData and browseVignettes('sesameData') for documentation
#> snapshotDate(): 2021-05-18
#> see ?sesameData and browseVignettes('sesameData') for documentation
#> [1] "cg18370151" "cg12460175" "cg14086922" "cg21463605"