RNA-Seq Workflow Vignette - library(airway) Missing "quants" directory
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dmbergau • 0
@bbbdbca0
Last seen 6 weeks ago
United States

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

RNASeq DESeq2 airway • 138 views
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Entering edit mode
@mikelove
Last seen 1 hour ago
United States

You are following the vignette on the website which is up to date but you are using a version of R / Bioconductor from ~2.5 years ago: April 2019.

This link below is the vignette that works with your version of R / Bioconductor, where you won't see the "quants" directory or any code relating to "quants":

https://bioconductor.org/packages/3.9/workflows/html/rnaseqGene.html

Alternatively, you can update to the latest version of R / Bioconductor if you want to follow the current workflows or vignettes (the ones you see on the website).

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