FilterContextCytosines {SingleMoleculeFootprinting} | R Documentation |
Filter Cytosines in context
FilterContextCytosines(MethGR, genome, context)
MethGR |
Granges obj of average methylation |
genome |
BSgenome |
context |
Context of interest (e.g. "GC", "CG",..) |
filtered Granges obj
Qinput = paste0(tempdir(), "/NRF1Pair_Qinput.txt") library(BSgenome.Mmusculus.UCSC.mm10) if(file.exists(Qinput)){ QuasRprj = GetQuasRprj(Qinput, BSgenome.Mmusculus.UCSC.mm10) Samples = readr::read_delim(Qinput, delim = "\t")$SampleName sample = Samples[1] range = GRanges(seqnames = "chr6", ranges = IRanges(start = 88106000, end = 88106500), strand = "*") MethGR = QuasR::qMeth(QuasRprj[grep(sample, Samples)], mode="allC", range, collapseBySample = TRUE, keepZero = TRUE) FilterContextCytosines(MethGR, BSgenome.Mmusculus.UCSC.mm10, "NGCNN") }