Open kcmtest opened 2 years ago
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?
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so how do we use that function? or any other way of doing it?
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
I'm trying to run GDCquery_Maf function
My code which i took from one of the tutorial
The error
Again I tried for my disease of interest which is AML I get the following error
How do i fix the issue?
Sessioninfo