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

Merged

kasperdanielhansen merged 10 commits into

hansenlab: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
SrenBlikdal
committed
1e2ec76
Add function (check_bedMethyl) to validate input for read.bedMethyl(). Adjust text in MethylCounts-class.Rd to fit the imported matrixes.
SrenBlikdal
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69ab725
include check of bedMethylfiles in read.bedMethyl and small improvements of the man files.
SrenBlikdal
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ee751e0
add #inline annotation to read.bedMethyl
SrenBlikdal
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16025c7
remove rmZeroCov from read.bedMethyl and update documentation
SrenBlikdal
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2885cb6
quick fix bug caused Cov being DelayedMatrix object when MethylCount is read as hdf5
SrenBlikdal
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7ca8dfb

Commits on Jan 30, 2026

add vingnettes with references to folder and add MethylCount as input for BSseq constructor function
SrenBlikdal
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dca8ac2

Commits on Feb 3, 2026

Commits on Feb 4, 2026

Fix small typo in bsseq.bib
SrenBlikdal
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5750742