vplagnol
commented
4 years ago mmm I recently updated ExomeDepth to 1.13 to deal with some new R compatibility issue, and something odd may be happening with tibbles and data frames. It could be that you need to update your dplyr package? Some incompatibility there?
For now, I have done created a version 1.1.14, that does
return(data.frame(exon_count_frame))
in getBamCounts so ideally you should not be bothered by the tibble issue anymore.
Can you please try:
> devtools::install_github("vplagnol/ExomeDepth")
and tell me what happens?
nelsonchanhk
Hello, I'm a new to ExomeDepth and is currently try it on my custom targeted capture panel. At the end of getBamCounts, the following error shows up.
Now parsing ~/OPERATION/RedCellNGS_hg19/BAM_testing/Normal9.bam Parsing chromosome chr1 Parsing chromosome chr10 Parsing chromosome chr11 Parsing chromosome chr12 Parsing chromosome chr13 Parsing chromosome chr14 Parsing chromosome chr15 Parsing chromosome chr16 Parsing chromosome chr17 Parsing chromosome chr18 Parsing chromosome chr19 Parsing chromosome chr2 Parsing chromosome chr20 Parsing chromosome chr21 Parsing chromosome chr22 Parsing chromosome chr3 Parsing chromosome chr4 Parsing chromosome chr5 Parsing chromosome chr6 Parsing chromosome chr7 Parsing chromosome chr8 Parsing chromosome chr9 Number of counted fragments : 836974 There were 50 or more warnings (use warnings() to see the first 50)
Furthermore, the output of getBamCounts in my case is a list and when I tried to convert it to a data frame, it failed with the following error.
My script is as follows. data(exons.hg19) hg19<-file.path("~/OPERATION/RedCellNGS_hg19/ref","hg19.fa") bamName <- list.files("~/OPERATION/RedCellNGS_hg19/BAM", pattern = '*.bam$') bamFile <- file.path("~/OPERATION/RedCellNGS_hg19/BAM",bamName) ExomeCount <- getBamCounts(bed.frame = exons.hg19,bam.files = bamFile,include.chr = TRUE,referenceFasta = hg19)
My sessionInfo() is as follows. R version 3.6.2 (2019-12-12) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.3 LTS
Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
locale: [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] ExomeDepth_1.1.13
loaded via a namespace (and not attached): [1] matrixStats_0.55.0 lattice_0.20-38
[3] IRanges_2.20.1 Rsamtools_2.2.1
[5] Biostrings_2.54.0 GenomicAlignments_1.22.1
[7] bitops_1.0-6 grid_3.6.2
[9] GenomeInfoDb_1.22.0 stats4_3.6.2
[11] magrittr_1.5 zlibbioc_1.32.0
[13] XVector_0.26.0 S4Vectors_0.24.1
[15] Matrix_1.2-18 aod_1.3.1
[17] BiocParallel_1.20.1 tools_3.6.2
[19] Biobase_2.46.0 RCurl_1.95-4.12
[21] DelayedArray_0.12.1 parallel_3.6.2
[23] compiler_3.6.2 BiocGenerics_0.32.0
[25] GenomicRanges_1.38.0 SummarizedExperiment_1.16.1 [27] GenomeInfoDbData_1.2.2
Thank you very much for your help!