GDCprepare: Prepare GDC data

In BioinformaticsFMRP/TCGAbiolinks: TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

Prepare GDC data

Description

Reads the data downloaded and prepare it into an R object

Usage

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")
)

Arguments

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"

Value

A summarizedExperiment or a data.frame

Author(s)

Tiago Chedraoui Silva

Examples

## 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)

BioinformaticsFMRP/TCGAbiolinks documentation built on April 12, 2024, 2:08 a.m.