Update read.bedMethyl() and alpha version of implementation for working with 5hmC and 5mC in bsseq()#155

Merged

kasperdanielhansen merged 10 commits intohansenlab:develfrom

SrenBlikdal:devel

Feb 6, 2026

Commits on Jan 20, 2026

Update functions and manuals to use MethylCounts object, shift the positions in the object by 1 but double check if it is inline with GRranges format
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Add function (check_bedMethyl) to validate input for read.bedMethyl(). Adjust text in MethylCounts-class.Rd to fit the imported matrixes.
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include check of bedMethylfiles in read.bedMethyl and small improvements of the man files.
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add #inline annotation to read.bedMethyl
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remove rmZeroCov from read.bedMethyl and update documentation
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quick fix bug caused Cov being DelayedMatrix object when MethylCount is read as hdf5
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Commits on Jan 30, 2026

add vingnettes with references to folder and add MethylCount as input for BSseq constructor function
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Commits on Feb 3, 2026

Commits on Feb 4, 2026

Fix small typo in bsseq.bib
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