DiffBind 3.0.9 missing bam files for vignette

Question

[t2]

Hello all, I saw that there is a new version of DiffBind from Bioconductor out with many updates and I wanted to test it out. I installed the package but am not able to run through the vignette because the reads directory is missing and there are no bam files. I downloaded using BiocManager.

The R version I'm running is 4.0.3 on linux.

My code so far:

setwd(system.file('extra',package='DiffBind'))
samples <- read.csv(file.path(system.file("extra", package="DiffBind"),"tamoxifen.csv"))
tamoxifen <- dba(sampleSheet=samples)
tamoxifen.count <- dba.count(tamoxifen)

Then I get a warning message that says the bam files are not accessible.

1: reads/Chr18_BT474_ER_1.bam not accessible 2: reads/Chr18_BT474_ER_2.bam not accessible 3: reads/Chr18_MCF7_ER_1.bam not accessible

I checked and the files are not accessible.

file.exists("reads/Chr18_BT474_ER_1.bam")
[1] FALSE

There is no 'reads' directory in '~/R/x86_64-pc-linux-gnu-library/4.0/DiffBind/extra/' which is where the 'peaks' directory is that contains the bed files. Can anyone please help me out so I can install and use the new DiffBind 3.0?

Thanks very much, Tesa

[rpolicastro]

Can you double check you have the correct version first with sessionInfo().

[t2]

session info gives:

R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.1 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               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    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] DiffBind_3.0.9              SummarizedExperiment_1.20.0 MatrixGenerics_1.2.0        matrixStats_0.57.0         
 [5] GenomicRanges_1.42.0        GenomeInfoDb_1.26.2         GSEABase_1.52.1             graph_1.68.0               
 [9] annotate_1.68.0             XML_3.99-0.5                AnnotationDbi_1.52.0        IRanges_2.24.1             
[13] S4Vectors_0.28.1            Biobase_2.50.0              BiocGenerics_0.36.0         singscore_1.10.0           

loaded via a namespace (and not attached):
  [1] GOstats_2.56.0           backports_1.2.1          BiocFileCache_1.14.0     plyr_1.8.6              
  [5] splines_4.0.3            BiocParallel_1.24.1      ggplot2_3.3.3            amap_0.8-18             
  [9] digest_0.6.27            invgamma_1.1             GO.db_3.12.1             SQUAREM_2020.5          
 [13] magrittr_2.0.1           checkmate_2.0.0          memoise_1.1.0            BSgenome_1.58.0         
 [17] base64url_1.4            limma_3.46.0             Biostrings_2.58.0        systemPipeR_1.24.2      
 [21] askpass_1.1              bdsmatrix_1.3-4          prettyunits_1.1.1        jpeg_0.1-8.1            
 [25] colorspace_2.0-0         blob_1.2.1               rappdirs_0.3.1           apeglm_1.12.0           
 [29] ggrepel_0.9.0            dplyr_1.0.2              crayon_1.3.4             RCurl_1.98-1.2          
 [33] jsonlite_1.7.2           hexbin_1.28.1            genefilter_1.72.0        brew_1.0-6              
 [37] survival_3.2-7           VariantAnnotation_1.36.0 glue_1.4.2               gtable_0.3.0            
 [41] zlibbioc_1.36.0          XVector_0.30.0           DelayedArray_0.16.0      V8_3.4.0                
 [45] Rgraphviz_2.34.0         scales_1.1.1             pheatmap_1.0.12          mvtnorm_1.1-1           
 [49] DBI_1.1.0                edgeR_3.32.0             Rcpp_1.0.5               xtable_1.8-4            
 [53] progress_1.2.2           emdbook_1.3.12           bit_4.0.4                rsvg_2.1                
 [57] AnnotationForge_1.32.0   truncnorm_1.0-8          httr_1.4.2               gplots_3.1.1            
 [61] RColorBrewer_1.1-2       ellipsis_0.3.1           pkgconfig_2.0.3          farver_2.0.3            
 [65] dbplyr_2.0.0             locfit_1.5-9.4           tidyselect_1.1.0         labeling_0.4.2          
 [69] rlang_0.4.10             reshape2_1.4.4           munsell_0.5.0            tools_4.0.3             
 [73] generics_0.1.0           RSQLite_2.2.1            stringr_1.4.0            yaml_2.2.1              
 [77] bit64_4.0.5              caTools_1.18.0           purrr_0.3.4              RBGL_1.66.0             
 [81] xml2_1.3.2               biomaRt_2.46.0           compiler_4.0.3           rstudioapi_0.13         
 [85] curl_4.3                 png_0.1-7                geneplotter_1.68.0       tibble_3.0.4            
 [89] stringi_1.5.3            GenomicFeatures_1.42.1   lattice_0.20-41          Matrix_1.3-0            
 [93] vctrs_0.3.6              pillar_1.4.7             lifecycle_0.2.0          BiocManager_1.30.10     
 [97] irlba_2.3.3              data.table_1.13.6        bitops_1.0-6             rtracklayer_1.50.0      
[101] R6_2.5.0                 latticeExtra_0.6-29      hwriter_1.3.2            ShortRead_1.48.0        
[105] KernSmooth_2.23-18       MASS_7.3-53              gtools_3.8.2             assertthat_0.2.1        
[109] DESeq2_1.30.0            openssl_1.4.3            Category_2.56.0          rjson_0.2.20            
[113] withr_2.3.0              GenomicAlignments_1.26.0 batchtools_0.9.14        Rsamtools_2.6.0         
[117] GenomeInfoDbData_1.2.4   hms_0.5.3                grid_4.0.3               tidyr_1.1.2             
[121] DOT_0.1                  coda_0.19-4              GreyListChIP_1.22.0      ashr_2.2-47             
[125] mixsqp_0.3-43            bbmle_1.0.23.1           numDeriv_2016.8-1.1

Answer 1

[rpolicastro]

According to the vignettte the BAM files are too big to include in the package. They have them hosted here for download.

[t2]

Ok, I don't know how I missed that in the vignette. Thanks so much!

[rpolicastro]

It was in a footnote, so it was easy to miss :)