readMethylome {MethylSeekR} | R Documentation |
Loading Bis-seq data from tab-delimited file or saved GRanges object
readMethylome(FileName, seqLengths, format = "text")
FileName |
File name. |
seqLengths |
A named vector indicating the chromosome lengths of the genome used. |
format |
File format. If format is set to "text" (default), the argument FileName should refer to a tab-delimited text file in the format: chromosome position T M, where each line stands for a CpG, the position refers to the C of the CpG (on the plus strand), T is the total number of reads (total counts) covering the CpG and M the total number of reads without C to T conversion at the C of the CpG (methylation counts). If format="GRanges", the file is assumed to be a GRanges object, containing T and M as first and second data-value entries, saved in rds format. |
A GRanges object containing the coordinates, total (T) and methylated counts (M)
Lukas Burger lukas.burger@fmi.ch
library(MethylSeekR) # get chromosome lengths library("BSgenome.Hsapiens.UCSC.hg18") sLengths=seqlengths(Hsapiens) # read methylation data methFname <- system.file("extdata", "Lister2009_imr90_hg18_chr22.tab", package="MethylSeekR") meth.gr <- readMethylome(FileName=methFname, seqLengths=sLengths)