Inconsistencies in drug names?

[bhaibeka]

Lack of consistency across functions: Lapatinib or lapatinib?

drugDoseResponseCurve(drug="Lapatinib", cellline="AU565", pSets=CCLE, plot.type="Actual", lwd=2, mycol="red", cex.main=1.3, cex=1.3, legend.loc=NA)

ss <- sensitivityInfo(CCLE)
which(apply(X=ss[ , c("cellid", "drugid")], MARGIN=1, FUN=function(x, y) { all(is.element(x, y)) }, y=c("AU565", "lapatinib")))

Depending on the function, the drug name must be different to extract the data

[ChristopherEeles]

Hi @bhaibeka,

How did you make the ss object? Without that information, I can't replicate the issue.

Best,
Chris

[bhaibeka]

My bad

ss <- sensitivityInfo(CCLE)

[ChristopherEeles]

Hi @bhaibeka,

When I run:

library(PharmacoGx)
CCLE <- downloadPSet('CCLE_2015')

ss <- sensitivityInfo(CCLE)
which(apply(X=ss[ , c("cellid", "drugid")], MARGIN=1, FUN=function(x, y) { all(is.element(x, y)) }, y=c("AU565", "lapatinib")))

I get back named integer(0), which indicates that 'lapatinib' does not match.

This is corroborated by:

unique(ss$drugid)

Which returns:

 [1] "Nvp-aew541"       "Nilotinib"        "Tanespimycin"     "Pha-665752"      
 [5] "Lapatinib"        "Nutlin-3"         "Saracatinib"      "Crizotinib"      
 [9] "L-685458"         "Vandetanib"       "Panobinostat"     "Sorafenib"       
[13] "Irinotecan"       "Topotecan"        "LBW242"           "PD-0325901"      
[17] "Palbociclib"      "Paclitaxel"       "Selumetinib"      "PLX4720"         
[21] "Raf265(chir-265)" "Nvp-tae 684"      "Dovitinib"        "Erlotinib"

So as far as I can tell, the drug is only referred to as 'Laptinib' in the PharmacoSet and therefore there is no discrepancy.

If you got a different result is it possible you were: (1) using an outdated version of CCLE or (2) using an outdated version of PharmacoGx?

My sessionInfo() is:

R Under development (unstable) (2021-02-24 r80033)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS

Matrix products: default
BLAS:   /opt/R/devel/lib/R/lib/libRblas.so
LAPACK: /opt/R/devel/lib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
 [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
 [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   

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

other attached packages:
[1] PharmacoGx_2.3.5 CoreGx_1.3.0    

loaded via a namespace (and not attached):
 [1] lsa_0.73.2                  bitops_1.0-6               
 [3] matrixStats_0.58.0          RColorBrewer_1.1-2         
 [5] GenomeInfoDb_1.27.8         SnowballC_0.7.0            
 [7] tools_4.1.0                 utf8_1.2.1                 
 [9] R6_2.5.0                    DT_0.17                    
[11] KernSmooth_2.23-18          sm_2.2-5.6                 
[13] DBI_1.1.1                   BiocGenerics_0.37.1        
[15] colorspace_2.0-0            tidyselect_1.1.0           
[17] gridExtra_2.3               curl_4.3                   
[19] compiler_4.1.0              Biobase_2.51.0             
[21] shinyjs_2.0.0               DelayedArray_0.17.10       
[23] slam_0.1-48                 caTools_1.18.2             
[25] scales_1.1.1                relations_0.6-9            
[27] stringr_1.4.0               digest_0.6.27              
[29] XVector_0.31.1              pkgconfig_2.0.3            
[31] htmltools_0.5.1.1           plotrix_3.8-1              
[33] MatrixGenerics_1.3.1        fastmap_1.1.0              
[35] limma_3.47.12               maps_3.3.0                 
[37] htmlwidgets_1.5.3           rlang_0.4.10               
[39] shiny_1.6.0                 visNetwork_2.0.9           
[41] generics_0.1.0              jsonlite_1.7.2             
[43] BiocParallel_1.25.5         gtools_3.8.2               
[45] dplyr_1.0.5                 RCurl_1.98-1.3             
[47] magrittr_2.0.1              GenomeInfoDbData_1.2.4     
[49] Matrix_1.3-2                Rcpp_1.0.6                 
[51] celestial_1.4.6             munsell_0.5.0              
[53] S4Vectors_0.29.9            fansi_0.4.2                
[55] lifecycle_1.0.0             stringi_1.5.3              
[57] piano_2.7.0                 MASS_7.3-53.1              
[59] SummarizedExperiment_1.21.1 zlibbioc_1.37.0            
[61] plyr_1.8.6                  gplots_3.1.1               
[63] grid_4.1.0                  parallel_4.1.0             
[65] promises_1.2.0.1            shinydashboard_0.7.1       
[67] crayon_1.4.1                lattice_0.20-41            
[69] mapproj_1.2.7               pillar_1.5.1               
[71] fgsea_1.17.0                tcltk_4.1.0                
[73] igraph_1.2.6                GenomicRanges_1.43.3       
[75] reshape2_1.4.4              marray_1.69.0              
[77] stats4_4.1.0                fastmatch_1.1-0            
[79] NISTunits_1.0.1             glue_1.4.2                 
[81] downloader_0.4              data.table_1.14.0          
[83] vctrs_0.3.7                 httpuv_1.5.5               
[85] gtable_0.3.0                RANN_2.6.1                 
[87] purrr_0.3.4                 assertthat_0.2.1           
[89] ggplot2_3.3.3               mime_0.10                  
[91] xtable_1.8-4                pracma_2.3.3               
[93] later_1.1.0.1               tibble_3.1.0               
[95] IRanges_2.25.6              sets_1.0-18                
[97] cluster_2.1.1               ellipsis_0.3.1             
[99] magicaxis_2.2.1

[bhaibeka]

I am using $.0.3 and PharmacoGx_2.2.4 CoreGx_1.2.0

I will upgrade to the last versions

[ChristopherEeles]

@bhaibeka,

That should be the most up-to-date release version of PharmacoGx, so you don't need to upgrade. I will try your code again in R 4.0.3 and see if the results differ.

Best,
Chris

[ChristopherEeles]

@bhaibeka,

I tested the code in R 4.0.3 and the results are the same. It looks like only 'Lapatinib' is used in the drugids of CCLE_2015. I also manually checked other instances where a column named drugid occur such as drugInfo(CCLE) and curation(CCLE)$drug and the drug name is consistent.

If you got a different result can you post what the function returns and your sessionInfo() so I can try to replicate it? Otherwise I will close this issue.

Best,
Chris

My sessionInfo() is:

R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)

Matrix products: default

locale:
[1] LC_COLLATE=English_Canada.1252  LC_CTYPE=English_Canada.1252   
[3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C                   
[5] LC_TIME=English_Canada.1252    

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

other attached packages:
[1] PharmacoGx_2.2.4 CoreGx_1.2.0    

loaded via a namespace (and not attached):
  [1] lsa_0.73.2                  bitops_1.0-6               
  [3] matrixStats_0.58.0          RColorBrewer_1.1-2         
  [5] GenomeInfoDb_1.26.4         SnowballC_0.7.0            
  [7] tools_4.0.3                 utf8_1.2.1                 
  [9] R6_2.5.0                    DT_0.17                    
 [11] KernSmooth_2.23-18          sm_2.2-5.6                 
 [13] DBI_1.1.1                   BiocGenerics_0.36.0        
 [15] colorspace_2.0-0            tidyselect_1.1.0           
 [17] gridExtra_2.3               curl_4.3                   
 [19] compiler_4.0.3              Biobase_2.50.0             
 [21] shinyjs_2.0.0               DelayedArray_0.16.3        
 [23] slam_0.1-48                 caTools_1.18.2             
 [25] scales_1.1.1                relations_0.6-9            
 [27] stringr_1.4.0               digest_0.6.27              
 [29] rmarkdown_2.7               XVector_0.30.0             
 [31] pkgconfig_2.0.3             htmltools_0.5.1.1          
 [33] plotrix_3.8-1               MatrixGenerics_1.2.1       
 [35] maps_3.3.0                  fastmap_1.1.0              
 [37] limma_3.46.0                htmlwidgets_1.5.3          
 [39] rlang_0.4.10                shiny_1.6.0                
 [41] visNetwork_2.0.9            generics_0.1.0             
 [43] jsonlite_1.7.2              BiocParallel_1.24.1        
 [45] gtools_3.8.2                dplyr_1.0.5                
 [47] RCurl_1.98-1.3              magrittr_2.0.1             
 [49] GenomeInfoDbData_1.2.4      Matrix_1.3-2               
 [51] celestial_1.4.6             Rcpp_1.0.6                 
 [53] munsell_0.5.0               S4Vectors_0.28.1           
 [55] fansi_0.4.2                 lifecycle_1.0.0            
 [57] stringi_1.5.3               piano_2.6.0                
 [59] yaml_2.2.1                  MASS_7.3-53.1              
 [61] SummarizedExperiment_1.20.0 zlibbioc_1.36.0            
 [63] plyr_1.8.6                  gplots_3.1.1               
 [65] grid_4.0.3                  parallel_4.0.3             
 [67] promises_1.2.0.1            shinydashboard_0.7.1       
 [69] crayon_1.4.1                lattice_0.20-41            
 [71] mapproj_1.2.7               knitr_1.31                 
 [73] pillar_1.5.1                tcltk_4.0.3                
 [75] fgsea_1.16.0                igraph_1.2.6               
 [77] GenomicRanges_1.42.0        reshape2_1.4.4             
 [79] marray_1.68.0               stats4_4.0.3               
 [81] fastmatch_1.1-0             NISTunits_1.0.1            
 [83] glue_1.4.2                  evaluate_0.14              
 [85] downloader_0.4              data.table_1.14.0          
 [87] BiocManager_1.30.12         vctrs_0.3.7                
 [89] httpuv_1.5.5                RANN_2.6.1                 
 [91] gtable_0.3.0                purrr_0.3.4                
 [93] assertthat_0.2.1            ggplot2_3.3.3              
 [95] xfun_0.21                   mime_0.10                  
 [97] xtable_1.8-4                pracma_2.3.3               
 [99] later_1.1.0.1               tibble_3.1.0               
[101] IRanges_2.24.1              sets_1.0-18                
[103] cluster_2.1.1               ellipsis_0.3.1             
[105] magicaxis_2.2.1

[p-smirnov]

@ChristopherEeles @bhaibeka I think the issue here may come from the CCLEsmall object provided as an example. I think it will still use the lower case "lapatinib", we have not updated it since the standardization of drug names.