LiNk-NY
commented
3 years ago Hi @afaissa,
Sorry but you would have to be more specific here. What do you mean by "all" patient data?
Please make sure that BiocManager::valid() is returning TRUE for you.
If the data that you are looking for is not present. You would have to provide a more detailed
report that includes the API endpoint for the data that you were expecting.
This is the clinical data table that I get back including a large number of variables.
> cbio <- cBioPortal()
> PatientData <- clinicalData(api = cbio, studyId = "luad_tcga")
> PatientData
# A tibble: 586 x 81
patientId AGE AJCC_METASTASIS_PATH… AJCC_NODES_PATHOL… AJCC_PATHOLOGIC_TU…
<chr> <chr> <chr> <chr> <chr>
1 TCGA-05-4… 70 M1 N2 Stage IV
2 TCGA-05-4… 81 M0 N2 Stage IIIA
3 TCGA-05-4… 67 M0 N0 Stage IB
4 TCGA-05-4… 79 M0 N1 Stage IIIA
5 TCGA-05-4… 68 M0 N0 Stage IB
6 TCGA-05-4… 66 M0 N2 Stage IIIA
7 TCGA-05-4… 70 M0 N0 Stage IA
8 TCGA-05-4… 58 M0 N0 Stage IB
9 TCGA-05-4… 76 M0 N2 Stage IIIB
10 TCGA-05-4… 76 M0 N1 Stage IIIB
[truncated...] You can also try clearing the cache by deleting the file listed from this command:
cBioPortalData:::.getHashCache(digest::digest(list("clinicalData", cbio, "luad_tcga")))Best, Marcel
afaissa
Hi Marcel,
Thank you for your feedback and sorry for the missing information.
Here the whole thing:
library(cBioPortalData) cbio <- cBioPortal() PatientData <- clinicalData(api = cbio, studyId = "luad_tcga")
There is a file for the environment here if you would like to check.
https://drive.google.com/file/d/15OWRvojEGOpYscKmQc6liM2CzAiPnhN9/view?usp=sharing
I understand the issue is on my R, but I would be happy to get some help.
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] parallel stats4 stats graphics grDevices utils datasets methods
[9] base
other attached packages: [1] Rsamtools_2.8.0 Biostrings_2.61.0
[3] XVector_0.33.0 cBioPortalData_2.5.1
[5] MultiAssayExperiment_1.19.1 SummarizedExperiment_1.23.0 [7] Biobase_2.53.0 GenomicRanges_1.45.0
[9] GenomeInfoDb_1.29.0 IRanges_2.27.0
[11] S4Vectors_0.31.0 BiocGenerics_0.39.0
[13] MatrixGenerics_1.5.0 matrixStats_0.58.0
[15] AnVIL_1.5.0 dplyr_1.0.6
[17] curl_4.3.1
loaded via a namespace (and not attached): [1] bitops_1.0-7 bit64_4.0.5 filelock_1.0.2
[4] progress_1.2.2 httr_1.4.2 GenomicDataCommons_1.17.0 [7] tools_4.1.0 utf8_1.2.1 R6_2.5.0
[10] DBI_1.1.1 withr_2.4.2 tidyselect_1.1.1
[13] prettyunits_1.1.1 TCGAutils_1.13.0 bit_4.0.4
[16] compiler_4.1.0 cli_2.5.0 rvest_1.0.0
[19] formatR_1.10 xml2_1.3.2 DelayedArray_0.19.0
[22] rtracklayer_1.53.0 readr_1.4.0 rappdirs_0.3.3
[25] rapiclient_0.1.3 RCircos_1.2.1 stringr_1.4.0
[28] digest_0.6.27 pkgconfig_2.0.3 dbplyr_2.1.1
[31] fastmap_1.1.0 limma_3.49.0 rlang_0.4.11
[34] RSQLite_2.2.7 BiocIO_1.3.0 generics_0.1.0
[37] jsonlite_1.7.2 BiocParallel_1.27.0 RCurl_1.98-1.3
[40] magrittr_2.0.1 GenomeInfoDbData_1.2.6 futile.logger_1.4.3
[43] Matrix_1.3-3 Rcpp_1.0.6 fansi_0.5.0
[46] lifecycle_1.0.0 stringi_1.6.2 yaml_2.2.1
[49] RaggedExperiment_1.17.0 RJSONIO_1.3-1.4 zlibbioc_1.39.0
[52] BiocFileCache_2.1.0 grid_4.1.0 blob_1.2.1
[55] crayon_1.4.1 lattice_0.20-44 splines_4.1.0
[58] GenomicFeatures_1.45.0 hms_1.1.0 KEGGREST_1.33.0
[61] pillar_1.6.1 rjson_0.2.20 biomaRt_2.49.0
[64] futile.options_1.0.1 XML_3.99-0.6 glue_1.4.2
[67] lambda.r_1.2.4 data.table_1.14.0 BiocManager_1.30.15
[70] vctrs_0.3.8 png_0.1-7 purrr_0.3.4
[73] tidyr_1.1.3 assertthat_0.2.1 cachem_1.0.5
[76] restfulr_0.0.13 survival_3.2-11 tibble_3.1.2
[79] RTCGAToolbox_2.23.1 GenomicAlignments_1.29.0 AnnotationDbi_1.55.0
[82] memoise_2.0.0 ellipsis_0.3.2
Originally posted by @afaissa in https://github.com/waldronlab/cBioPortalData/issues/42#issuecomment-851682010