Order CpGs by genomic location

Source: R/util1_OrderCpGsByLocation.R

Order CpGs by genomic location

OrderCpGsByLocation(
  CpGs_char,
  genome = c("hg19", "hg38"),
  arrayType = c("450k", "EPIC"),
  manifest_gr = NULL,
  ignoreStrand = TRUE,
  output = c("vector", "dataframe")
)

Arguments

CpGs_char

vector of CpGs

genome

Human genome of reference: hg19 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

output

vector of CpGs or dataframe with CpGs, CHR, MAPINFO

Value

vector of CpGs ordered by location or dataframe with CpGs ordered by location (cpg), chromosome (chr), position (pos)

Examples


 CpGs_char <- c("cg04677227", "cg07146435", "cg11632906", "cg20214853")
 OrderCpGsByLocation(
   CpGs_char,
   genome = "hg19",
   arrayType = "450k",
   ignoreStrand = TRUE,
   output = "dataframe"
 )
#> snapshotDate(): 2021-05-18
#> see ?sesameData and browseVignettes('sesameData') for documentation
#>     chr       pos        cpg
#> 1 chr10 100028236 cg20214853
#> 2 chr10 100028320 cg04677227
#> 3 chr10 100028468 cg11632906
#> 4 chr10 100028499 cg07146435