documentation does not reflect latest 1.1.15 changes

[jamigo]

where it says name = ExomeCount.dafr$names it should say name = ExomeCount.dafr$exon in here https://github.com/vplagnol/ExomeDepth/blob/0c93b6e43589280f8e925782f5b65c5e5ac2e5c6/vignette/vignette.Rnw#L243 with all dependencies up to date.

also, is the transition.probability = 10^-4 value still recommended? other users are working with higher values (such as 10^-3, or even DeCon's 10^-2). any thoughts on this?

[vplagnol]

Thanks @jamigo . I will fix it now, apologies for missing this.

[vplagnol]

Actually... I don't see it sorry. See attached screenshot of the vignette. Is this an issue of package version?

[jamigo]

what I meant is that once you update not only ExomeDepth but also its dependencies something happens. unfortunately I'm no expert in the dependencies' modules, but I think there could be a column name changed in the GenomicRanges object, although I don't find any documentation about it and it looks like a problem on my side.

this is what I get following the vignette's 3.1 step on a small my.bam file:

> library(ExomeDepth)
> data(exons.hg19)
> my.counts<-getBamCounts(bed.frame = exons.hg19, bam.files = "my.bam", include.chr = FALSE)
> head(my.counts)
  chromosome start   end         exon my.bam
1          1 35139 35174    FAM138A_3      0
2          1 35278 35481    FAM138A_2      0
3          1 35722 35736    FAM138A_1      0
4          1 53050 53067 AL627309.2_1      0
5          1 54831 54936 AL627309.2_2      0
6          1 69092 70008      OR4F5_1      0

as you see, the column name "exon" is the former "names".

this is my environment, in case it helps:

> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.5 (Maipo)

Matrix products: default
BLAS/LAPACK: /mnt/netapp1/Optcesga_FT2_RHEL7/easybuild-cesga/software/Core/imkl/2018.5.274/compilers_and_libraries_2018.5.274/linux/mkl/lib/intel64_lin/libmkl_gf_lp64.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] grid      stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] ExomeDepth_1.1.15

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.3                  XVector_0.26.0
 [3] magrittr_1.5                GenomicRanges_1.38.0
 [5] BiocGenerics_0.32.0         zlibbioc_1.32.0
 [7] GenomicAlignments_1.22.1    IRanges_2.20.2
 [9] tidyselect_1.0.0            BiocParallel_1.20.1
[11] lattice_0.20-38             R6_2.4.1
[13] rlang_0.4.5                 GenomeInfoDb_1.22.0
[15] dplyr_0.8.4                 tools_3.6.0
[17] SummarizedExperiment_1.16.1 parallel_3.6.0
[19] Biobase_2.46.0              matrixStats_0.55.0
[21] assertthat_0.2.1            tibble_2.1.3
[23] crayon_1.3.4                Matrix_1.2-17
[25] GenomeInfoDbData_1.2.2      purrr_0.3.3
[27] S4Vectors_0.24.3            bitops_1.0-6
[29] RCurl_1.95-4.12             aod_1.3.1
[31] glue_1.3.1                  DelayedArray_0.12.2
[33] pillar_1.4.3                compiler_3.6.0
[35] Rsamtools_2.2.3             Biostrings_2.54.0
[37] stats4_3.6.0                pkgconfig_2.0.3

I'd be really grateful if you'd be able to give some advice. and as I said, if it's a problem on my side, please feel free to close this issue.