Hi there, I am using QDNAseq to call CNA in sWGS data. Initial results showed CNAs in centromeres areas of several chromosomes, recurrently in all samples (benign and tumor samples). I am trying to mask centromeres and telomeres, following the instructions:

bins$blacklist = calculateBlacklist(bins, bedFiles = c("hg38blacklist.v2.bed", "centromeres_region_hg38.bed",
"GAPlocations_hg38.bed"))

I have tried those files, and also downloaded the ones shown in the tutorial (http://bioconductor.org/packages/release/bioc/vignettes/QDNAseq/inst/doc/QDNAseq.pdf ;page 12)

bins$blacklist = calculateBlacklist(bins, bedFiles = c("/Downloads/wgEncodeDacMapabilityConsensusExcludable.bed",
"/Downloads/wgEncodeDukeMapabilityRegionsExcludable.bed"))

##The error is the same;
##...Error in as.vector(data) :
##no method for coercing this S4 class to a vector

I checked calculateBlacklist(), tried step by step and the error appears at the end, when it tries to merge blacklist within bins object (Large AnnotateDataFrame):

blacklist <- future.apply::future_apply(bins, MARGIN = 1L, FUN = overlap.counter,
joined = joined)
##"Error in as.vector(data) :
##no method for coercing this S4 class to a vector"

##Bins were obtained:
bins <- getBinAnnotations(binSize=50, genome="hg38")

Any idea of how to fix the error?

Thanks!