Error in .checkFixSampleMap(sampleMap)

[shbrief]

Hi! I'm getting the below error for my query:

> cbio_api <- cBioPortal()
> study <- "aml_ohsu_2018"
> samples <- c("aml_ohsu_2018_16-00374", "aml_ohsu_2018_16-00783")
> cBioPortalData(
+     api = cbio_api,
+     by = "hugoGeneSymbol",
+     studyId = study,
+     sampleIds = samples,
+     genePanelId = "Agilent"
+ )
Error in .checkFixSampleMap(sampleMap) : 
  'sampleMap' does not have required columns

What are the required columns?

Here is the session info:

R Under development (unstable) (2025-01-20 r87609)
Platform: aarch64-unknown-linux-gnu
Running under: Ubuntu 24.04.1 LTS

Matrix products: default
BLAS:   /usr/lib/aarch64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/aarch64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Etc/UTC
tzcode source: system (glibc)

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

other attached packages:
 [1] cBioPortalData_2.19.9           MultiAssayExperiment_1.33.4     AnVIL_1.19.8                    AnVILBase_1.1.0                
 [5] curatedMetagenomicData_3.15.0   TreeSummarizedExperiment_2.15.0 Biostrings_2.75.3               XVector_0.47.2                 
 [9] SingleCellExperiment_1.29.1     SummarizedExperiment_1.37.0     Biobase_2.67.0                  GenomicRanges_1.59.1           
[13] GenomeInfoDb_1.43.4             IRanges_2.41.2                  S4Vectors_0.45.2                BiocGenerics_0.53.5            
[17] generics_0.1.3                  MatrixGenerics_1.19.1           matrixStats_1.5.0               OmicsMLRepoR_1.1.0             
[21] dplyr_1.1.4                    

loaded via a namespace (and not attached):
  [1] ggtext_0.1.2                fs_1.6.5                    bitops_1.0-9                DirichletMultinomial_1.49.0
  [5] lubridate_1.9.4             httr_1.4.7                  RColorBrewer_1.1-3          GenomicDataCommons_1.31.0  
  [9] tools_4.5.0                 backports_1.5.0             utf8_1.2.4                  DT_0.33                    
 [13] R6_2.5.1                    vegan_2.6-8                 lazyeval_0.2.2              mgcv_1.9-1                 
 [17] permute_0.9-7               withr_3.0.2                 TCGAutils_1.27.6            gridExtra_2.3              
 [21] cli_3.6.3                   textshaping_1.0.0           formatR_1.14                sandwich_3.1-1             
 [25] slam_0.1-55                 mvtnorm_1.3-3               readr_2.1.5                 rapiclient_0.1.8           
 [29] Rsamtools_2.23.1            systemfonts_1.2.1           yulab.utils_0.1.9           foreign_0.8-88             
 [33] stringdist_0.9.15           scater_1.35.0               decontam_1.27.0             parallelly_1.41.0          
 [37] readxl_1.4.3                fillpattern_1.0.2           rstudioapi_0.17.1           RSQLite_2.3.9              
 [41] BiocIO_1.17.1               visNetwork_2.1.2            vroom_1.6.5                 rbiom_2.0.13               
 [45] Matrix_1.7-2                futile.logger_1.4.3         ggbeeswarm_0.7.2            DECIPHER_3.3.2             
 [49] abind_1.4-8                 lifecycle_1.0.4             yaml_2.3.10                 RaggedExperiment_1.31.1    
 [53] biocViews_1.75.0            SparseArray_1.7.4           BiocFileCache_2.15.1        grid_4.5.0                 
 [57] blob_1.2.4                  promises_1.3.2              ExperimentHub_2.15.0        crayon_1.5.3               
 [61] miniUI_0.1.1.1              lattice_0.22-6              beachmat_2.23.6             GenomicFeatures_1.59.1     
 [65] KEGGREST_1.47.0             pillar_1.10.1               knitr_1.49                  rjson_0.2.23               
 [69] boot_1.3-31                 estimability_1.5.1          lpSolve_5.6.23              codetools_0.2-20           
 [73] glue_1.8.0                  data.table_1.16.4           vctrs_0.6.5                 png_0.1-8                  
 [77] treeio_1.31.0               Rdpack_2.6.2                cellranger_1.1.0            gtable_0.3.6               
 [81] cachem_1.1.0                xfun_0.50                   mime_0.12                   rbibutils_2.3              
 [85] S4Arrays_1.7.1              reformulas_0.4.0            RTCGAToolbox_2.37.2         DiagrammeR_1.0.11          
 [89] bluster_1.17.0              nlme_3.1-166                bit64_4.6.0-1               filelock_1.0.3             
 [93] data.tree_1.1.0             irlba_2.3.5.1               vipor_0.4.7                 rpart_4.1.24               
 [97] colorspace_2.1-1            DBI_1.2.3                   Hmisc_5.2-2                 nnet_7.3-20                
[101] tidyselect_1.2.1            processx_3.8.5              emmeans_1.10.6              bit_4.5.0.1                
[105] compiler_4.5.0              curl_6.2.0                  rvest_1.0.4                 httr2_1.1.0                
[109] graph_1.85.1                BiocCheck_1.43.2            htmlTable_2.4.3             BiocNeighbors_2.1.2        
[113] xml2_1.3.6                  DelayedArray_0.33.4         rtracklayer_1.67.0          checkmate_2.3.2            
[117] scales_1.3.0                RBGL_1.83.0                 callr_3.7.6                 rappdirs_0.3.3             
[121] stringr_1.5.1               digest_0.6.37               minqa_1.2.8                 rmarkdown_2.29             
[125] htmltools_0.5.8.1           pkgconfig_2.0.3             base64enc_0.1-3             lme4_1.1-36                
[129] sparseMatrixStats_1.19.0    dbplyr_2.5.0                fastmap_1.2.0               rlang_1.1.5                
[133] htmlwidgets_1.6.4           UCSC.utils_1.3.1            shiny_1.10.0                DelayedMatrixStats_1.29.1  
[137] farver_2.1.2                zoo_1.8-12                  jsonlite_1.8.9              BiocParallel_1.41.0        
[141] BiocSingular_1.23.0         RCurl_1.98-1.16             magrittr_2.0.3              Formula_1.2-5              
[145] scuttle_1.17.0              GenomeInfoDbData_1.2.13     patchwork_1.3.0             munsell_0.5.1              
[149] Rcpp_1.0.14                 ape_5.8-1                   ggnewscale_0.5.0            viridis_0.6.5              
[153] stringi_1.8.4               zlibbioc_1.53.0             RJSONIO_1.3-1.9             MASS_7.3-64                
[157] AnnotationHub_3.15.0        plyr_1.8.9                  mediation_4.5.0             parallel_4.5.0             
[161] ggrepel_0.9.6               splines_4.5.0               gridtext_0.1.5              hms_1.1.3                  
[165] ps_1.8.1                    igraph_2.1.4                RUnit_0.4.33                reshape2_1.4.4             
[169] ScaledMatrix_1.15.0         futile.options_1.0.1        BiocVersion_3.21.1          XML_3.99-0.18              
[173] evaluate_1.0.3              lambda.r_1.2.4              BiocManager_1.30.25         httpuv_1.6.15              
[177] nloptr_2.1.1                tzdb_0.4.0                  rols_3.3.0                  tidyr_1.3.1                
[181] purrr_1.0.2                 ggplot2_3.5.1               BiocBaseUtils_1.9.0         rsvd_1.0.5                 
[185] xtable_1.8-4                restfulr_0.0.15             tidytree_0.4.6              later_1.4.1                
[189] viridisLite_0.4.2           ragg_1.3.3                  tibble_3.2.1                GenomicAlignments_1.43.0   
[193] memoise_2.0.1               beeswarm_0.4.0              AnnotationDbi_1.69.0        cluster_2.1.8              
[197] timechange_0.3.0            mia_1.15.6   

[LiNk-NY]

Hi Sehyun, @shbrief

You should include a molecularProfileIds input.
But even with a molecularProfileId, it returns an empty dataset.

suppressPackageStartupMessages({
    library(cBioPortalData)
})
cbio_api <- cBioPortal()
study <- "aml_ohsu_2018"
samples <- c("aml_ohsu_2018_16-00374", "aml_ohsu_2018_16-00783")
cBioPortalData(
    api = cbio_api,
    by = "hugoGeneSymbol",
    molecularProfileIds = "aml_ohsu_2018_rna_seq_mrna",
    studyId = study,
    sampleIds = samples,
    genePanelId = "Agilent"
)
#> Warning: No data found for molecularProfileId: aml_ohsu_2018_rna_seq_mrna
#> Error in .checkFixSampleMap(sampleMap): 'sampleMap' does not have required columns

^{Created on 2025-01-27 with reprex v2.1.1}