Question: Error in sort(abs(diff(genomdat)))[1:n.keep]
5.3 years ago by
Guest User • 12k
Guest User • 12k wrote:
Hi all, I'm using a package ExomeCNV to call LOH and got an error in step "Combine multiple positions into LOH segments" the.loh = multi.LOH.analyze(normal, tumor, all.loh.ls=list(eLOH), test.alpha=0.001, method="variance.f", sdundo=c(0,0), alpha=c(0.5,0.1)) Analyzing: Sample.1 Error in sort(abs(diff(genomdat)))[1:n.keep] : only 0's may be mixed with negative subscripts In addition: Warning message: In CNA(data$baf, strip.chr.name(data$chr), data$position, data.type = "binary") : markers with missing chrom and/or maploc removed ExomeCNV actually implement package DNAcopy in this step, and I can't tell how to bypass this problem since the "n.keep" isn't from ExomeCNV's code. I would really appreciate your expertise, thank you. -- output of sessionInfo(): R version 3.0.1 (2013-05-16) Platform: x86_64-w64-mingw32/x64 (64-bit) locale:  LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C  LC_TIME=English_United States.1252 attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  ExomeCNV_1.4 DNAcopy_1.34.0 BiocInstaller_1.10.1 loaded via a namespace (and not attached):  tools_3.0.1 -- Sent via the guest posting facility at bioconductor.org.
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