Running issue #1
Description
Hello,
When I have both segment (copy number) and SNV on VAF as input files to run the function run.absCNSeq(), it never gets run through. Please see the error message below
my.res.list <- run.absCNSeq("Pri.cnv.inputAbsCN.txt", "Pri.snp.inputAbsCN.txt", res.dir, "Pri", seq.type="WES", min.seg.len=200)
Error in .local(x, ...) : no rows to aggregate
Note that the file format according to the input file instruction.
When I only input one segment file, some samples work, some samples have the error message below, please let me know how to correct the files or scripts to make the program work.
my.res.list <- run.absCNSeq("4095-1.cnv.inputAbsCN.txt", snv.fn=NULL, res.dir, "4095-1", seq.type="WES", min.seg.len=200)
Error in .local(x, ...) : no rows to aggregate
Thanks so much,
EL
sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.1 (El Capitan)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] doMC_1.3.4 iterators_1.0.8 foreach_1.4.3 ABSOLUTE_1.0.6
[5] numDeriv_2014.2-1 absCNseq_1.0 ggplot2_2.0.0 BubbleTree_2.1.8
[9] magrittr_1.5 dplyr_0.4.3 plyr_1.8.3 GenomicRanges_1.22.2
[13] GenomeInfoDb_1.6.1 IRanges_2.4.6 S4Vectors_0.8.5 BiocGenerics_0.16.1
loaded via a namespace (and not attached):
[1] rgl_0.95.1435 Rcpp_0.12.2 biovizBase_1.18.0
[4] mvtnorm_1.0-3 lattice_0.20-33 gtools_3.5.0
[7] Rsamtools_1.22.0 class_7.3-14 Biostrings_2.38.2
[10] digest_0.6.8 assertthat_0.1 R6_2.1.1
[13] futile.options_1.0.0 acepack_1.3-3.3 WriteXLS_4.0.0
[16] pcaPP_1.9-60 RSQLite_1.0.0 e1071_1.6-7
[19] rainbow_3.3 zlibbioc_1.16.0 GenomicFeatures_1.22.7
[22] lazyeval_0.1.10 misc3d_0.8-4 rpart_4.1-10
[25] splines_3.2.3 BiocParallel_1.4.3 foreign_0.8-66
[28] RCurl_1.95-4.7 biomaRt_2.26.1 munsell_0.4.2
[31] rtracklayer_1.30.1 nnet_7.3-11 multicool_0.1-9
[34] SummarizedExperiment_1.0.1 gridExtra_2.0.0 hdrcde_3.1
[37] Hmisc_3.17-1 codetools_0.2-14 XML_3.98-1.3
[40] GenomicAlignments_1.6.1 MASS_7.3-45 bitops_1.0-6
[43] grid_3.2.3 gtable_0.1.2 DBI_0.3.1
[46] scales_0.3.0 KernSmooth_2.23-15 XVector_0.10.0
[49] limma_3.26.3 latticeExtra_0.6-26 futile.logger_1.4.1
[52] Formula_1.2-1 BiocStyle_1.8.0 lambda.r_1.1.7
[55] RColorBrewer_1.1-2 tools_3.2.3 dichromat_2.0-0
[58] BSgenome_1.38.0 Biobase_2.30.0 ks_1.10.0
[61] survival_2.38-3 AnnotationDbi_1.32.3 colorspace_1.2-6
[64] cluster_2.0.3 VariantAnnotation_1.16.4