Genomic ranges found in CEEHRC bedgraph files is 0 based instead of 1 based ranges used in R

[helimelie]

HI,

I am using WGBS methylation data from CEEHRC project through DeppBlueR package and visualise it using Gviz. First track is a HM450 probes. Second track is obviously the bases sequence of the genome. Third track is WGBS.

When plotting these data at high resolution I can see that the methylation data are 1 base left of where it should be (aligned with GC instead of the following CG), as I understand the data and as I can see in UCSC genome browser: (you can find gaphs here with the code to generate it: https://support.bioconductor.org/p/109472/
experiment_name= "A34409.3_lanes_dupsFlagged.q5.f0.5mC.CpG.fractional.bedgraph"
)

I guess that this is because bedgraph data uses 0 based genomic coordinates while R uses 1 based ranges.

I posted this question on Bioconductor forum and another user identified as Markus suggested me to report the bug here.

Thanks

Mel