summarizeMolecularProfiles not working

[shwetha141]

Hello, I was trying to work with the code uploaded and for some reason I get this error when I run summarizeMolecularProfiles

Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘summarizeMolecularProfiles’ for signature ‘"missing"’

[ChristopherEeles]

Hi @shwetha141,

Please provide the code you are trying to run so I can help you debug.

Best,
Christopher Eeles
Software Developer
Haibe-Kains Lab
PM-Research | UHN

[shwetha141]

Hi Chris, apologies for the delay. I was trying to follow with a tutorial that was posted and some of the function didn't seem to be working. I do see that there is an updated vignette for this package. I will try to refer it for my analysis.
https://github.com/Bioconductor/BiocWorkshops/blob/master/260_Safikhani_Pharmacogenomics.Rmd

[ChristopherEeles]

Hi @shwetha141,

That workshop is pretty old and we have made a number of changes to PharmacoGx since it was published.

One key different is that we changed the nomenclature of our PharmacoSet objects in the downloadPSet function to allow for new releases of the same data (i.e., data versioning).

If you view the availablePSets() table, the "PSet Name" column indicates the value that should be passed to downloadPSet to retrieve the associated data object.

From the error your included previously, it looks like the PSets are not being downloaded. If you update the data set names for the downloads the rest of the code should (theoretically) work.

Best,
Chris

[shwetha141]

Thank you so much. I am sorry for asking such redundant questions. I am quite new to bioinformatics and assessing drug response is even newer to me. I was wondering if you can suggest something for the kind of analysis I would like to do. I am looking at the drug sensitivity of cell lines with specific mutations, e.g TP53 mutations. I did try to assess the sensitivity cut-off using the waterfall analysis but I am not sure how to interpret it. The paper suggests that I use the inflection point of the curve to be the cut-off but the Coregx mentions something else. Do you have any suggestions? Conversely, I can also cell lines that are sensitive to a p53 pathway target (https://www.cancerrxgene.org/cellline/22RV1/924100) and assess their molecular profiles, something like this ( https://cellmodelpassports.sanger.ac.uk/passports/SIDM01240). Is there a way I can do this for a group of cell lines. Thank you, sorry for the long email. Shwetha

…

On Thu, Nov 3, 2022 at 10:32 AM Christopher Eeles ***@***.***> wrote: Hi @shwetha141 <https://github.com/shwetha141>, That workshop is pretty old and we have made a number of changes to PharmacoGx since it was published. One key different is that we changed the nomenclature of our PharmacoSet objects in the downloadPSet function to allow for new releases of the same data (i.e., data versioning). If you view the availablePSets() table, the "PSet Name" column indicates the value that should be passed to downloadPSet to retrieve the associated data object. From the error your included previously, it looks like the PSets are not being downloaded. If you update the data set names for the downloads the rest of the code should (theoretically) work. — Reply to this email directly, view it on GitHub <#124 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AETL4GS6TRCQGEB6BLIVYPLWGPLKBANCNFSM54EZLNEA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[shwetha141]

I am running the codes posted
https://github.com/RomaHD/DrugRespPrediction/blob/master/analysis1/data_for_analysis1.R
I am afraid I am getting the same error for summarizeMolecularProfiles which

Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘summarizeMolecularProfiles’ for signature ‘"missing"’

_session info
R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)

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] stats4 stats graphics grDevices utils datasets methods base

other attached packages:
[1] org.Hs.eg.db_3.15.0 AnnotationDbi_1.58.0 PharmacoGx_3.0.2
[4] CoreGx_2.0.2 SummarizedExperiment_1.26.1 Biobase_2.56.0
[7] GenomicRanges_1.48.0 GenomeInfoDb_1.32.4 IRanges_2.30.1
[10] S4Vectors_0.34.0 MatrixGenerics_1.8.1 matrixStats_0.62.0
[13] BiocGenerics_0.42.0

loaded via a namespace (and not attached):
[1] fgsea_1.22.0 colorspace_2.0-3 ellipsis_0.3.2
[4] lsa_0.73.3 XVector_0.36.0 rstudioapi_0.14
[7] SnowballC_0.7.0 MultiAssayExperiment_1.22.0 DT_0.26
[10] bit64_4.0.5 fansi_1.0.3 codetools_0.2-18
[13] cachem_1.0.6 jsonlite_1.8.3 magicaxis_2.2.14
[16] cluster_2.1.4 png_0.1-7 shinydashboard_0.7.2
[19] shiny_1.7.3 httr_1.4.4 mapproj_1.2.9
[22] compiler_4.2.1 backports_1.4.1 assertthat_0.2.1
[25] Matrix_1.5-1 fastmap_1.1.0 bench_1.1.2
[28] limma_3.52.4 cli_3.3.0 later_1.3.0
[31] visNetwork_2.1.2 htmltools_0.5.3 tools_4.2.1
[34] igraph_1.3.5 gtable_0.3.1 glue_1.6.2
[37] GenomeInfoDbData_1.2.8 RANN_2.6.1 reshape2_1.4.4
[40] dplyr_1.0.10 maps_3.4.1 fastmatch_1.1-3
[43] Rcpp_1.0.9 slam_0.1-50 Biostrings_2.64.1
[46] vctrs_0.4.2 BumpyMatrix_1.4.0 stringr_1.4.1
[49] mime_0.12 lifecycle_1.0.3 gtools_3.9.3
[52] zlibbioc_1.42.0 MASS_7.3-58.1 scales_1.2.1
[55] promises_1.2.0.1 relations_0.6-12 parallel_4.2.1
[58] RColorBrewer_1.1-3 sets_1.0-21 memoise_2.0.1
[61] gridExtra_2.3 ggplot2_3.3.6 downloader_0.4
[64] stringi_1.7.8 RSQLite_2.2.18 NISTunits_1.0.1
[67] plotrix_3.8-2 checkmate_2.1.0 caTools_1.18.2
[70] boot_1.3-28 BiocParallel_1.30.4 rlang_1.0.6
[73] pkgconfig_2.0.3 bitops_1.0-7 pracma_2.4.2
[76] lattice_0.20-45 htmlwidgets_1.5.4 bit_4.0.4
[79] tidyselect_1.2.0 plyr_1.8.7 magrittr_2.0.3
[82] R6_2.5.1 gplots_3.1.3 generics_0.1.3
[85] DelayedArray_0.22.0 DBI_1.1.3 sm_2.2-5.7.1
[88] pillar_1.8.1 KEGGREST_1.36.3 RCurl_1.98-1.9
[91] tibble_3.1.8 crayon_1.5.2 KernSmooth_2.23-20
[94] utf8_1.2.2 grid_4.2.1 data.table_1.14.4
[97] marray_1.74.0 blob_1.2.3 piano_2.12.1
[100] digest_0.6.30 xtable_1.8-4 httpuv_1.6.6
[103] coop_0.6-3 munsell_0.5.0 celestial_1.4.6
[106] shinyjs_2.1.0_

[ChristopherEeles]

Hi @shwetha141,

That code is very old and PharmacoGx has been updated several times since that code ran. The solution has already been discussed in #130, but the issue is the argument names for most PharmacoGx functions have changed from pSet to object.

If you make that change it should resolve your current error. However, that code appears to be very old and we cannot guarantee backwards compatibility beyond a year or two.

That being said, Bioconductor archives old package releases. As such if you cannot get the script working you can find the Bioconductor release from when that code was last updated and install the appropriate packages like: BiocManager::install(version="<old version>"), where you replace the angle bracket porition with the appropriate Bioconductor release version.

Best,
Christopher Eeles
Software Developer
Haibe-Kains Lab
Princess Margaret Cancer Centre

[shwetha141]

Thank you Christopher, I am really sorry. I should have checked the prior issues.
Apologies for the oversight. I looked up and assumed PSet and object were interchangeable. I looked at the documentation and missed that point.

https://www.bioconductor.org/packages/devel/bioc/manuals/PharmacoGx/man/PharmacoGx.pdf

[gadepallivs]

@ChristopherEeles What is the equivalent function for the PharmacoGx::cellInfo(object)$Expression.arrays ? I get Error: object 'cellInfo' is not exported by 'namespace:PharmacoGx'

[ChristopherEeles]

Hi @gadepallivs,

The cellInfo function was renamed to sampleInfo and moved into CoreGx (which is automatically loaded with PharmacoGx).

Best,
Chris