GDCprepare | R Documentation |
Reads the data downloaded and prepare it into an R object
GDCprepare(
query,
save = FALSE,
save.filename,
directory = "GDCdata",
summarizedExperiment = TRUE,
remove.files.prepared = FALSE,
add.gistic2.mut = NULL,
mutant_variant_classification = c("Frame_Shift_Del", "Frame_Shift_Ins",
"Missense_Mutation", "Nonsense_Mutation", "Splice_Site", "In_Frame_Del",
"In_Frame_Ins", "Translation_Start_Site", "Nonstop_Mutation")
)
query |
A query for GDCquery function |
save |
Save result as RData object? |
save.filename |
Name of the file to be save if empty an automatic will be created |
directory |
Directory/Folder where the data was downloaded. Default: GDCdata |
summarizedExperiment |
Create a summarizedExperiment? Default TRUE (if possible) |
remove.files.prepared |
Remove the files read? Default: FALSE This argument will be considered only if save argument is set to true |
add.gistic2.mut |
If a list of genes (gene symbol) is given, columns with gistic2 results from GDAC firehose (hg19) and a column indicating if there is or not mutation in that gene (hg38) (TRUE or FALSE - use the MAF file for more information) will be added to the sample matrix in the summarized Experiment object. |
mutant_variant_classification |
List of mutant_variant_classification that will be consider a sample mutant or not. Default: "Frame_Shift_Del", "Frame_Shift_Ins", "Missense_Mutation", "Nonsense_Mutation", "Splice_Site", "In_Frame_Del", "In_Frame_Ins", "Translation_Start_Site", "Nonstop_Mutation" |
A summarizedExperiment or a data.frame
Tiago Chedraoui Silva
## Not run:
query <- GDCquery(
project = "TCGA-KIRP",
data.category = "Simple Nucleotide Variation",
data.type = "Masked Somatic Mutation"
)
GDCdownload(query, method = "api", directory = "maf")
maf <- GDCprepare(query, directory = "maf")
## End(Not run)
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