Static QC Updates for new GDSC Pset

[raymond126]

Static QC checks:

1. summarizeSensitivityProfiles()
   Error:
   [CoreGx::assay] There is no assay profiles in this LongTable. Use assayNames(longTable) for a listof valid assay names.

2. assay() returns characters instead of numeric values
   rna_seq <-assay(GDSC_2020v2@molecularProfiles@ExperimentList$rnaseq.tpm)
   str(rna_seq)
   chr [1:37313, 1:949] "0.44" "5.09" "19.18" "5.7" ...

• attr(*, "dimnames")=List of 2
  ..$ : chr [1:37313] "A1BG" "A1BG-AS1" "A1CF" "A2M" ...
  ..$ : chr [1:949] "22RV1" "23132-87" "42-MG-BA" "451LU" ...

3. subsetTo() not working
   camptothecin <- subsetTo(GDSC_2020v2, drug = "Camptothecin")
   Error in as.list.default(X) :
   no method for coercing this S4 class to a vector

Session Info:
R version 4.3.0 (2023-04-21)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.2.1

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0

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

other attached packages:
[1] gridExtra_2.3
[2] forcats_1.0.0
[3] devtools_2.4.5
[4] usethis_2.2.2
[5] ggExtra_0.10.1
[6] magick_2.8.2
[7] jpeg_0.1-10
[8] cowplot_1.1.3
[9] ggpubr_0.6.0
[10] dplyr_1.1.4
[11] ggplot2_3.4.4
[12] PharmacoGx_3.4.0
[13] CoreGx_2.4.0
[14] SummarizedExperiment_1.30.2
[15] Biobase_2.60.0
[16] GenomicRanges_1.52.1
[17] GenomeInfoDb_1.36.4
[18] IRanges_2.34.1
[19] S4Vectors_0.38.2
[20] MatrixGenerics_1.12.3
[21] matrixStats_1.2.0
[22] BiocGenerics_0.46.0

loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3
[2] rstudioapi_0.15.0
[3] jsonlite_1.8.8
[4] MultiAssayExperiment_1.26.0
[5] magrittr_2.0.3
[6] rmarkdown_2.25
[7] fs_1.6.3
[8] zlibbioc_1.46.0
[9] vctrs_0.6.5
[10] memoise_2.0.1
[11] magicaxis_2.4.5
[12] RCurl_1.98-1.14
[13] rstatix_0.7.2
[14] htmltools_0.5.7
[15] S4Arrays_1.0.6
[16] plotrix_3.8-4
[17] broom_1.0.5
[18] pracma_2.4.4
[19] KernSmooth_2.23-22
[20] htmlwidgets_1.6.4
[21] plyr_1.8.9
[22] cachem_1.0.8
[23] igraph_2.0.1.1
[24] mime_0.12
[25] lifecycle_1.0.4
[26] piano_2.16.0
[27] pkgconfig_2.0.3
[28] Matrix_1.6-5
[29] R6_2.5.1
[30] fastmap_1.1.1
[31] GenomeInfoDbData_1.2.10
[32] shiny_1.8.0
[33] digest_0.6.34
[34] colorspace_2.1-0
[35] pkgload_1.3.4
[36] SnowballC_0.7.1
[37] fansi_1.0.6
[38] abind_1.4-5
[39] coop_0.6-3
[40] compiler_4.3.0
[41] remotes_2.4.2.1
[42] withr_3.0.0
[43] downloader_0.4
[44] marray_1.78.0
[45] backports_1.4.1
[46] BiocParallel_1.34.2
[47] carData_3.0-5
[48] bench_1.1.3
[49] pkgbuild_1.4.3
[50] gplots_3.1.3.1
[51] maps_3.4.2
[52] ggsignif_0.6.4
[53] MASS_7.3-60.0.1
[54] sessioninfo_1.2.2
[55] DelayedArray_0.26.7
[56] gtools_3.9.5
[57] caTools_1.18.2
[58] tools_4.3.0
[59] NISTunits_1.0.1
[60] httpuv_1.6.14
[61] relations_0.6-13
[62] glue_1.7.0
[63] promises_1.2.1
[64] checkmate_2.3.1
[65] cluster_2.1.6
[66] reshape2_1.4.4
[67] fgsea_1.26.0
[68] generics_0.1.3
[69] gtable_0.3.4
[70] sm_2.2-5.7.1
[71] tidyr_1.3.1
[72] data.table_1.15.2
[73] car_3.1-2
[74] utf8_1.2.4
[75] XVector_0.40.0
[76] RANN_2.6.1
[77] pillar_1.9.0
[78] stringr_1.5.1
[79] limma_3.56.2
[80] BumpyMatrix_1.8.0
[81] later_1.3.2
[82] lattice_0.22-5
[83] tidyselect_1.2.0
[84] miniUI_0.1.1.1
[85] knitr_1.45
[86] xfun_0.41
[87] shinydashboard_0.7.2
[88] DT_0.31
[89] visNetwork_2.1.2
[90] stringi_1.8.3
[91] yaml_2.3.8
[92] boot_1.3-28.1
[93] evaluate_0.23
[94] codetools_0.2-19
[95] lsa_0.73.3
[96] tibble_3.2.1
[97] cli_3.6.2
[98] xtable_1.8-4
[99] munsell_0.5.0
[100] Rcpp_1.0.12
[101] mapproj_1.2.11
[102] parallel_4.3.0
[103] sets_1.0-25
[104] ellipsis_0.3.2
[105] profvis_0.3.8
[106] urlchecker_1.0.1
[107] bitops_1.0-7
[108] slam_0.1-50
[109] celestial_1.4.6
[110] scales_1.3.0
[111] purrr_1.0.2
[112] crayon_1.5.2
[113] rlang_1.1.3
[114] fastmatch_1.1-4
[115] shinyjs_2.1.0

[jjjermiah]

Hi @raymond126 thanks for this.

To start, can you please update your PharmacoGx from Github, there have been some developments since the biocondunctor release

remotes::install_github(
    "bhklab/PharmacoGx", 
    build_manual=TRUE, 
    build_vignettes=TRUE
)

1. This seems to be an error in the pipeline since I named the assay profiles_recomputed

2. This is a good catch, thanks. If you do check other assays, note that some of them purposefully use characters instead of integers to mark features i.e mutations/fusions

3. I'll have to debug subsetTo but for now can you use subsetBySample and subsetByTreatment to subset PSets and also try Camptothecin as CAMPTOTHECIN

I will let you know once the psets are updated.

In the future can you submit issues to the relevant Pipeline Repository instead in the Data-Processing Repository i.e for GDSC submit the issue at https://github.com/BHKLAB-DataProcessing/GDSC-Pharmacoset_Snakemake

[jjjermiah]

@raymond126 let me know if these worked with the new psets