SplitCpGDFbyRegion: Split CpG dataframe by Subregion

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

Split CpG dataframe by Subregion

Description

Split a dataframe of CpGs and comethylated subregions to a list of CpGs in each subregion

Usage

SplitCpGDFbyRegion(
  CpGsSubregions_df,
  genome = c("hg19", "hg38"),
  arrayType = c("450k", "EPIC"),
  manifest_gr = NULL,
  returnAllCpGs = TRUE
)

Arguments

CpGsSubregions_df	data frame with CpG and subregion number
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.
returnAllCpGs	indicates if outputting all the CpGs in the region when there is not a contiguous comethylated region or only the CpGs in the contiguous comethylated regions

Value

a list of comethylated subregions CpGs for a pre-defined region

Examples

   data(betaMatrix_ex4)
   CpGs_df <- MarkComethylatedCpGs(betaCluster_mat = betaMatrix_ex4)
   CpGsSubregions_df <- FindComethylatedRegions(CpGs_df)

   SplitCpGDFbyRegion(
     CpGsSubregions_df,
     genome = "hg19",
     arrayType = "450k"
   )

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