I am using PureCN, v1.6.3. it seems everything including predict somatic, get copy number and etc, go well except callLOH function. below is the standard error and session info, could you please help? thanks
below is the error information in stderr
In .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
Error in `$<-.data.frame`(`*tmp*`, "arm", value = "p") :
replacement has 1 row, data has 0
Calls: callLOH -> .getArmLocations -> $<- -> $<-.data.frame
Execution halted
below is the session infor
> sessionInfo()
R version 3.3.1 Patched (2016-08-12 r71089)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.3 (Santiago)
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] PureCN_1.6.3 VariantAnnotation_1.20.3
[3] Rsamtools_1.24.0 Biostrings_2.40.2
[5] XVector_0.12.1 SummarizedExperiment_1.2.3
[7] Biobase_2.32.0 GenomicRanges_1.26.4
[9] GenomeInfoDb_1.10.3 IRanges_2.8.2
[11] S4Vectors_0.12.2 BiocGenerics_0.20.0
[13] DNAcopy_1.48.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.12 RColorBrewer_1.1-2 futile.logger_1.4.3
[4] plyr_1.8.4 GenomicFeatures_1.24.5 bitops_1.0-6
[7] futile.options_1.0.0 tools_3.3.1 zlibbioc_1.18.0
[10] biomaRt_2.28.0 RSQLite_1.0.0 gtable_0.2.0
[13] BSgenome_1.40.1 DBI_0.7 rtracklayer_1.32.2
[16] grid_3.3.1 data.table_1.10.4 AnnotationDbi_1.34.4
[19] XML_3.98-1.4 BiocParallel_1.6.6 VGAM_1.0-3
[22] ggplot2_2.1.0 lambda.r_1.1.9 scales_0.4.1
[25] GenomicAlignments_1.8.4 splines_3.3.1 colorspace_1.2-6
[28] RCurl_1.95-4.8 munsell_0.4.3
