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?