View source: R/util3_SplitCpGsSubregionsDataFrameToList.R
SplitCpGDFbyRegion | R Documentation |
Split a dataframe of CpGs and comethylated subregions to a list of CpGs in each subregion
SplitCpGDFbyRegion( CpGsSubregions_df, genome = c("hg19", "hg38"), arrayType = c("450k", "EPIC"), manifest_gr = NULL, returnAllCpGs = TRUE )
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
|
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 |
a list of comethylated subregions CpGs for a pre-defined region
data(betaMatrix_ex4) CpGs_df <- MarkComethylatedCpGs(betaCluster_mat = betaMatrix_ex4) CpGsSubregions_df <- FindComethylatedRegions(CpGs_df) SplitCpGDFbyRegion( CpGsSubregions_df, genome = "hg19", arrayType = "450k" )
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