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  • Error in ExomeCNV running

    Hi all

    I want to use ExomeCNV to call CNV from my NGS result


    But when I try I got this kind of error

    > library(ExomeCNV)
    Loading required package: DNAcopy
    > chr.list=paste("chr",c("1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19","20","21","22","X","Y"),sep="")
    > normal_set1 = read.coverage.gatk("test_res1/set1_d/coverage/1532SD.REF_Y.sample_interval_summary")
    > tumor_set1 = read.coverage.gatk("test_res1/set1_d/coverage/1768.REF_Y.sample_interval_summary")
    > logR_set1 = calculate.logR(normal_set1,tumor_set1)
    > eCNV_set1 = c()
    > for (i in 1:length(chr.list)) {
    + idx = (normal_set1$chr = chr.list[i])
    + ecnv = classify.eCNV(normal=normal_set1[idx,], tumor=tumor_set1[idx,], logR=logR_set1[idx], min.spec=0.9999, min.sens=0.9999, option="spec", c=0.5, l=70)
    + eCNV_set1 = rbind(eCNV_set1,ecnv)
    + }
    [1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
    [1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
    [1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
    [1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
    [1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
    [1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
    [1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
    [1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
    [1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
    [1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
    [1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
    [1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
    [1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
    [1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
    [1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
    [1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
    [1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
    [1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
    [1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
    [1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
    [1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
    [1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
    [1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
    [1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
    > cnv_set1 = multi.CNV.analyze(normal_set1, tumor_set1, logR=logR_set1, all.cnv.ls=list(eCNV_set1), coverage.cutoff=5, min.spec=0.99, min.sens=0.99, option="auc", c=0.5)
    Error in sort(abs(diff(genomdat)))[1:n.keep] :
    only 0's may be mixed with negative subscripts
    Calls: multi.CNV.analyze -> CNV.analyze -> smooth.CNA -> trimmed.variance
    In addition: Warning message:
    In CNA(norm.log.ratio[well.covered.exon.idx], strip.chr.name(normal$chr[well.covered.exon.idx]), :
    markers with missing chrom and/or maploc removed

    Execution halted

    The example data in tutorial works well

    So, It seems that my data has a problem, But I couldn't find what's wrong

    Any kind of advice would be welcome

    Thanks

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