BSdata-class: Class "BSdata"

Description Objects from the Class Slots Author(s) See Also Examples


This class is used in the methylPipe library to point to a TABIX compressed file containing base-resolution DNA-methylation data and reference genome sequence

Objects from the Class

Objects can be created by calls of the form new("BSdata", ...) or using the function BSdata(file, uncov, org) whose arguments are described in the next section Slots.



Object of class "character" : the TABIX compressed file containing base-resolution DNA-methylation data. This file can be generated through the BSprepare function, and it must contain the following columns: chromosome assignment (in the form chr1, chr2...), genomic position (positive integer), strand (either - or +), methylation sequence context (either CG, CHG or CHH), number (>0) of sequencing reads with C calls at that genomic position, number of sequencing reads with T calls at that genomic position, binomial pvalue (-10*log10(pvalue)) for calling a mC at that position.


Object of class GRanges : this GRanges object consists of the list of genomic regions with sequencing coverage information; this information is used to distinguish which methylation sites are unmethylated, but covered, from those that are missing data since they have no sequencing coverage. This object is automatically generated by the function while processing aligned files generated from the aligner.


refrence genome of class BSgenome


Mattia Pelizzola

See Also



H1data <- system.file('extdata', 'H1_chr20_CG_10k_tabix_out.txt.gz', package='methylPipe')
uncov_GR <- GRanges(Rle('chr20'), IRanges(c(14350,69251,84185), c(18349,73250,88184)))
H1.db <- BSdata(file=H1data, uncov=uncov_GR, org=Hsapiens)

Search within the methylPipe package
Search all R packages, documentation and source code

Questions? Problems? Suggestions? or email at

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.