CpG coverage with MEDIPS
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greta • 0
Last seen 9 days ago

Hello! I'm trying to evaluate the enrichment of CpG in a MBD-seq experiment. I've used MEDIPS package, but when I've tried to apply the MEDIPS.CpGenrich function on an input file I've obtained this warning:

BSgenome="BSgenome" #this genome was generated with BSgenome package usign the function forgeBSgenomeDataPkg

> er = MEDIPS.CpGenrich(file = "S2.fastq.gz.bam", BSgenome = BSgenome, extend = extend, shift = shift, uniq = uniq)
Reading bam alignment S2.fastq.gz.bam 
Total number of imported short reads: 34296732
Extending reads...
Creating GRange Object...
Keep at most one 1 read mapping to the same genomic location.
Number of remaining reads: 19765414
Loading chromosome lengths for BSgenome...
Calculating CpG density for given regions...
Avvertimento: number of items to replace is not a multiple of replacement lengthAvvertimento: 'length(x)' is not a multiple of 'NROW(value)'Error in h(simpleError(msg, call)) : 
  errore durante la valutazione dell'argomento 'x' nella selezione di un metodo per la funzione 'XStringSet': solving row 3: 'allow.nonnarrowing' is FALSE and the supplied start (63761) is > refwidth + 1

sessionInfo( )
R version 4.3.0 (2023-04-21 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22621)

I'm not able to understand how I can fix this error. Could you please help me find a solution? Thanks in advance for your attention Greta

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