exomeCopy warning and error
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0
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@0986ff45
Last seen 5 weeks ago
Sweden

I'm getting a warning message and then an error when I run exomeCopy. Can you please help me with that? How it can be fixed?

``> fit.list <- lapply(sample.names, function(sample.name) {

  • lapply(seqlevels(target), function(seq.name) {
  • exomeCopy(counts[seqnames(counts) == seq.name],
  • sample.name, X.names = c("log.bg", "GC", "GC.sq", "width"), S = 0:4, d = 2)
  • })
  • }) Warning message: In exomeCopy(counts[seqnames(counts) == seq.name], sample.name, : More than 90% of sample counts are zero, exomeCopy will return NULL

    compiled.segments <- compileCopyCountSegments(fit.list) Error in FUN(X[[i]], ...) : trying to get slot "path" from an object of a basic class ("NULL") with no slots sessionInfo() R version 4.1.2 (2021-11-01) Platform: x86_64-suse-linux-gnu (64-bit) Running under: openSUSE Leap 15.1

Matrix products: default BLAS: /usr/lib64/R/lib/libRblas.so LAPACK: /usr/lib64/R/lib/libRlapack.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base

other attached packages: [1] exomeCopy_1.36.0 Rsamtools_2.6.0 Biostrings_2.58.0
[4] XVector_0.30.0 GenomicRanges_1.42.0 GenomeInfoDb_1.26.7 [7] IRanges_2.24.1 S4Vectors_0.28.1 BiocGenerics_0.36.1

loaded via a namespace (and not attached): [1] crayon_1.4.1 bitops_1.0-7 zlibbioc_1.36.0
[4] rstudioapi_0.13 BiocParallel_1.24.1 tools_4.1.2
[7] RCurl_1.98-1.3 compiler_4.1.2 GenomeInfoDbData_1.2.4

```

exomeCopy • 71 views
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@mikelove
Last seen 9 hours ago
United States

I'm guessing this data has too many zeros to produce a meaningful HMM output.

I would examine your data by eye, it may not be model-able with exomeCopy.

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