TCGAbiolinks
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BioinformaticsFMRP
GDCquery_Maf not working
I'm trying to run GDCquery_Maf function
My code which i took from one of the tutorial
library(TCGAbiolinks)
library(maftools)
packageVersion("TCGAbiolinks")
[1] ‘2.22.4’
The error
Error in GDCquery(paste0("TCGA-", tumor), data.category = "Simple Nucleotide Variation", : Please set a valid workflow.type argument from the list below:
=> Aliquot Ensemble Somatic Variant Merging and Masking
Traceback:
1. GDCquery_Maf("COAD", pipelines = "muse")
2. GDCquery(paste0("TCGA-", tumor), data.category = "Simple Nucleotide Variation",
. data.type = "Masked Somatic Mutation", workflow.type = workflow.type,
. access = "open")
3. stop("Please set a valid workflow.type argument from the list below:\n => ",
. paste(unique(results$analysis_workflow_type), collapse = "\n => "))
Again I tried for my disease of interest which is AML I get the following error
Error in GDCquery(paste0("TCGA-", tumor), data.category = "Simple Nucleotide Variation", : Please set a valid workflow.type argument from the list below:
=> Aliquot Ensemble Somatic Variant Merging and Masking
Traceback:
1. GDCquery_Maf("LAML", pipelines = "muse")
2. GDCquery(paste0("TCGA-", tumor), data.category = "Simple Nucleotide Variation",
. data.type = "Masked Somatic Mutation", workflow.type = workflow.type,
. access = "open")
3. stop("Please set a valid workflow.type argument from the list below:\n => ",
. paste(unique(results$analysis_workflow_type), collapse = "\n => "))
How do i fix the issue?
$platform
'x86_64-conda-linux-gnu'
$arch
'x86_64'
$os
'linux-gnu'
$system
'x86_64, linux-gnu'
$status
''
$major
'4'
$minor
'1.2'
$year
'2021'
$month
'11'
$day
'01'
$`svn rev`
'81115'
$language
'R'
$version.string
'R version 4.1.2 (2021-11-01)'
$nickname
'Bird Hippie'
Sessioninfo
R version 4.1.2 (2021-11-01)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /home/punit/anaconda3/envs/r_4.1.2/lib/libopenblasp-r0.3.20.so
locale:
[1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C
[3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8
[5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8
[7] LC_PAPER=en_US.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] maftools_2.10.05 TCGAbiolinks_2.22.4
loaded via a namespace (and not attached):
[1] bitops_1.0-7 matrixStats_0.62.0
[3] bit64_4.0.5 RColorBrewer_1.1-3
[5] filelock_1.0.2 progress_1.2.2
[7] httr_1.4.2 GenomeInfoDb_1.30.1
[9] repr_1.1.4 tools_4.1.2
[11] utf8_1.2.2 R6_2.5.1
[13] DBI_1.1.2 BiocGenerics_0.40.0
[15] colorspace_2.0-3 tidyselect_1.1.2
[17] prettyunits_1.1.1 bit_4.0.4
[19] curl_4.3.2 compiler_4.1.2
[21] cli_3.3.0 rvest_1.0.2
[23] Biobase_2.54.0 xml2_1.3.3
[25] DelayedArray_0.20.0 scales_1.2.0
[27] readr_2.1.2 rappdirs_0.3.3
[29] pbdZMQ_0.3-7 stringr_1.4.0
[31] digest_0.6.29 R.utils_2.11.0
[33] XVector_0.34.0 base64enc_0.1-3
[35] pkgconfig_2.0.3 htmltools_0.5.2
[37] MatrixGenerics_1.6.0 dbplyr_2.1.1
[39] fastmap_1.1.0 rlang_1.0.2
[41] RSQLite_2.2.13 generics_0.1.2
[43] jsonlite_1.8.0 dplyr_1.0.9
[45] R.oo_1.24.0 RCurl_1.98-1.6
[47] magrittr_2.0.3 GenomeInfoDbData_1.2.7
[49] Matrix_1.4-1 Rcpp_1.0.8.3
[51] IRkernel_1.3 munsell_0.5.0
[53] S4Vectors_0.32.4 fansi_1.0.3
[55] lifecycle_1.0.1 R.methodsS3_1.8.1
[57] stringi_1.7.6 SummarizedExperiment_1.24.0
[59] zlibbioc_1.40.0 plyr_1.8.7
[61] BiocFileCache_2.2.1 grid_4.1.2
[63] blob_1.2.3 crayon_1.5.1
[65] lattice_0.20-45 splines_4.1.2
[67] IRdisplay_1.1 Biostrings_2.62.0
[69] hms_1.1.1 KEGGREST_1.34.0
[71] knitr_1.39 pillar_1.7.0
[73] GenomicRanges_1.46.1 uuid_1.1-0
[75] TCGAbiolinksGUI.data_1.14.1 biomaRt_2.50.3
[77] stats4_4.1.2 XML_3.99-0.9
[79] glue_1.6.2 evaluate_0.15
[81] downloader_0.4 data.table_1.14.2
[83] png_0.1-7 vctrs_0.4.1
[85] tzdb_0.3.0 gtable_0.3.0
[87] purrr_0.3.4 tidyr_1.2.0
[89] assertthat_0.2.1 cachem_1.0.6
[91] ggplot2_3.3.5 xfun_0.30
[93] survival_3.3-1 tibble_3.1.6
[95] AnnotationDbi_1.56.2 memoise_2.0.1
[97] IRanges_2.28.0 ellipsis_0.3.2 `
```
Hi, GDCquery_Maf was removed from the latest version of the package after GDC last update.
On Sun, May 1, 2022, 5:14 PM krushnach80 @.***> wrote:
I'm trying to run GDCquery_Maf function
My code which i took from one of the tutorial
library(TCGAbiolinks)
library(maftools)
packageVersion("TCGAbiolinks")
[1] ‘2.22.4’
The error
Error in GDCquery(paste0("TCGA-", tumor), data.category = "Simple Nucleotide Variation", : Please set a valid workflow.type argument from the list below:
=> Aliquot Ensemble Somatic Variant Merging and Masking
Traceback:
GDCquery_Maf("COAD", pipelines = "muse")
GDCquery(paste0("TCGA-", tumor), data.category = "Simple Nucleotide Variation",
. data.type = "Masked Somatic Mutation", workflow.type = workflow.type,
. access = "open")
- stop("Please set a valid workflow.type argument from the list below:\n => ",
. paste(unique(results$analysis_workflow_type), collapse = "\n => "))
Again I tried for my disease of interest which is AML I get the following error
Error in GDCquery(paste0("TCGA-", tumor), data.category = "Simple Nucleotide Variation", : Please set a valid workflow.type argument from the list below:
=> Aliquot Ensemble Somatic Variant Merging and Masking
Traceback:
GDCquery_Maf("LAML", pipelines = "muse")
GDCquery(paste0("TCGA-", tumor), data.category = "Simple Nucleotide Variation",
. data.type = "Masked Somatic Mutation", workflow.type = workflow.type,
. access = "open")
- stop("Please set a valid workflow.type argument from the list below:\n => ",
. paste(unique(results$analysis_workflow_type), collapse = "\n => "))
How do i fix the issue?
— Reply to this email directly, view it on GitHub https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/511, or unsubscribe https://github.com/notifications/unsubscribe-auth/AABDQ6NT5ERG5JIORSJDG73VH3X2ZANCNFSM5U2NPIZQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>
Here is the documentation. https://bioconductor.org/packages/release/bioc/vignettes/TCGAbiolinks/inst/doc/mutation.html
Here is the documentation. https://bioconductor.org/packages/release/bioc/vignettes/TCGAbiolinks/inst/doc/mutation.html
let me read it
Hi, sorry for bumping into the old thread. Does the GDCquery function also support using different pipelines options such as muse, varscan2, somaticsniper, mutect. I only see the default parameters in the vignette and have no knowledge what else I could use. I use the following code to pull the MAF:
query <- GDCquery( project = "TCGA-LAML", data.category = "Simple Nucleotide Variation", access = "open", data.type = "Masked Somatic Mutation", workflow.type = "Aliquot Ensemble Somatic Variant Merging and Masking" ) GDCdownload(query) maf <- GDCprepare(query)
Best, Christian
