When trying to run the code at https://www.bioconductor.org/packages/devel/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html part of the vignette, the "quants" subdirectory is missing from the "airway" pacakge:
library("airway")
The R function system.file can be used to find out where on your computer the files from a package have been installed. Here we ask for the full path to the extdata directory, where R packages store external data, that is part of the airway package.
dir <- system.file("extdata", package="airway", mustWork=TRUE)
In this directory, we find a number of files, including eight BAM files that were used in the previous version of this workflow demonstrating alignment and counting. We will focus on the two directories that are in the quants directory, which contain the output from Salmon on two files.
list.files(dir)
[1] "GSE52778_series_matrix.txt" "Homo_sapiens.GRCh37.75_subset.gtf"
[3] "sample_table.csv" "SraRunInfo_SRP033351.csv"
[5] "SRR1039508_subset.bam" "SRR1039509_subset.bam"
[7] "SRR1039512_subset.bam" "SRR1039513_subset.bam"
[9] "SRR1039516_subset.bam" "SRR1039517_subset.bam"
[11] "SRR1039520_subset.bam" "SRR1039521_subset.bam"
list.files(file.path(dir, "quants"))
character(0)
As seen above, the "quants" directory is missing
sessionInfo()
R version 3.6.0 (2019-04-26) Platform: i386-w64-mingw32/i386 (32-bit) Running under: Windows >= 8 (build 9200)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] reticulate_1.20 limma_3.40.6 DESeq2_1.24.0
[4] airway_1.4.0 SummarizedExperiment_1.14.1 DelayedArray_0.10.0
[7] BiocParallel_1.18.1 matrixStats_0.58.0 Biobase_2.44.0
[10] GenomicRanges_1.36.1 GenomeInfoDb_1.20.0 IRanges_2.18.3
[13] S4Vectors_0.22.1 BiocGenerics_0.30.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 Formula_1.2-4 knitr_1.36 XVector_0.24.0
[5] magrittr_2.0.1 cluster_2.1.2 splines_3.6.0 zlibbioc_1.30.0
[9] bit_4.0.4 tidyselect_1.1.1 xtable_1.8-4 colorspace_2.0-1
[13] lattice_0.20-38 R6_2.5.1 rlang_0.4.12 jpeg_0.1-8.1
[17] fansi_0.4.2 xfun_0.28 latticeExtra_0.6-29 genefilter_1.66.0
[21] ellipsis_0.3.2 htmltools_0.5.2 bit64_4.0.5 assertthat_0.2.1
[25] digest_0.6.29 tibble_3.1.1 lifecycle_1.0.1 Matrix_1.3-3
[29] RCurl_1.98-1.3 cachem_1.0.4 compiler_3.6.0 pillar_1.6.4
[33] scales_1.1.1 backports_1.2.1 Hmisc_4.5-0 generics_0.1.1
[37] locfit_1.5-9.4 jsonlite_1.7.2 annotate_1.62.0 pkgconfig_2.0.3
[41] AnnotationDbi_1.46.1 rstudioapi_0.13 munsell_0.5.0 fastmap_1.1.0
[45] blob_1.2.2 dplyr_1.0.6 stringr_1.4.0 tools_3.6.0
[49] grid_3.6.0 nnet_7.3-16 htmlTable_2.3.0 data.table_1.14.0
[53] gtable_0.3.0 checkmate_2.0.0 png_0.1-7 utf8_1.2.1
[57] DBI_1.1.1 yaml_2.2.1 survival_3.2-11 crayon_1.4.2
[61] GenomeInfoDbData_1.2.1 gridExtra_2.3 geneplotter_1.62.0 purrr_0.3.4
[65] ggplot2_3.3.5 RColorBrewer_1.1-2 bitops_1.0-7 htmlwidgets_1.5.4
[69] base64enc_0.1-3 vctrs_0.3.8 rpart_4.1-15 memoise_2.0.1
[73] RSQLite_2.2.7 glue_1.4.2 stringi_1.6.1 XML_3.99-0.3
[77] foreign_0.8-76
