I have downloaded a BiSulfite-Seq dataset from Encode, which is only in wig format, with the first few lines as following :
track type=wiggle_0 name="UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.Bisulfite-Seq.skin03:methRatio" visibility=full color=20,150,20 altColor=150,20,20 windowingFunction=mean
In the description page in GEO, it mentions that the 2nd column are Methylation proportions.
I would like to read in this data into MethylSeekR, as I wish to identify LMR, FMR and UMRs. So far, after searching around in the internet and the package manual I am unable to find a way to do this. I tried using the readMethylome function, but it mentions that ( I am copying and pasting ):
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.
Is there a way to get T and M from the wig file ? Or any other way to read in the data to use the package ?