search

ccagc / QDNAseq

QDNAseq package for Bioconductor
47 stars 27 forks source link

Blacklisted regions in applyFilter function without providing a bed file #128

Open alexvasilikop opened 3 months ago

alexvasilikop commented 3 months ago

Hello,

I was wondering which regions QDNAseq is using by default in applyFilters is used with the option blacklist = TRUE. We are using it like the following without providing any BED files for the blacklisted regions. Are there some regions blacklisted by default ? ( I noticed some are missing after applying the filters).

readCounts <- binReadCounts(bins, bamfiles = InputFile)
readCounts <- estimateCorrection(readCounts)
readCounts <- applyFilters(readCounts, residual = TRUE, blacklist = TRUE, chromosomes = NA)    # includes both X & Y
copyNumbers <- correctBins(readCounts)
copyNumbersNormalized <- normalizeBins(copyNumbers)
copyNumbersSmooth <- smoothOutlierBins(copyNumbersNormalized)

Thanks