OrderCpGsByLocation: Order CpGs by genomic location

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

Order CpGs by genomic location

Description

Order CpGs by genomic location

Usage

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"
 )

TransBioInfoLab/coMethDMR documentation built on Oct. 15, 2024, 12:52 a.m.