R/MMRFprepare.R

In MarzyUnicz/MMRFBiolinksX:

#' @title Prepare GDC data
#' @description
#'   Reads the data downloaded and prepare it into an R object
#' @param query A query for GDCquery function
#' @param save Save result as RData object?
#' @param save.filename Name of the file to be save if empty an automatic will be created
#' @param directory Directory/Folder where the data was downloaded. Default: GDCdata
#' @param summarizedExperiment Create a summarizedExperiment? Default TRUE (if possible)
#' @param remove.files.prepared Remove the files read? Default: FALSE
#' This argument will be considered only if save argument is set to true
#' @param 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.
#' @param mut.pipeline If add.gistic2.mut is not NULL this field will be taken in consideration.
#' Four separate variant calling pipelines are implemented for GDC data harmonization.
#' Options: muse, varscan2, somaticsniper, MuTect2. For more information:
#' https://gdc-docs.nci.nih.gov/Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline/
#' @param 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"
#' @export
#' @examples
#' \dontrun{
#' query.mm.fpkm <- GDCquery(project = "MMRF-COMMPASS",
#'                           data.category = "Transcriptome Profiling",
#'                           data.type = "Gene Expression Quantification",
#'                           workflow.type="HTSeq - FPKM")
#'
#'
#' GDCdownload(query.mm.fpkm, method = "api", files.per.chunk = 100)
#' DataGDC.prep <- GDCprepare(query.mm.fpkm,
#'                            save = TRUE ,
#'                            save.filename = "MMCompassFPKM.rda" ,
#'                            directory = "GDCdata" ,
#'                            summarizedExperiment = TRUE)
#' }
#' @return A summarizedExperiment or a data.frame
#' @importFrom  S4Vectors DataFrame
#' @importFrom SummarizedExperiment metadata<-
#' @importFrom data.table setcolorder setnames
#' @importFrom GenomicRanges GRanges
#' @importFrom IRanges IRanges

MMRFprepare <- function(query,
                       save = FALSE,
                       save.filename,
                       directory = "GDCdata",
                       summarizedExperiment = TRUE,
                       remove.files.prepared = FALSE,
                       add.gistic2.mut = NULL,
                       mut.pipeline = "mutect2",
                       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")){



  object<-TCGAbiolinks::GDCprepare(query,
                                   save,
                                   save.filename,
                                   directory,
                                   summarizedExperiment,
                                   remove.files.prepared,
                                   add.gistic2.mut,
                                   mut.pipeline,
                                   mutant_variant_classification)








  definition<-SummarizedExperiment::colData(object)$sample_type
  definition <- as.data.frame(definition)
  SummarizedExperiment::colData(object) <- cbind(SummarizedExperiment::colData(object), definition)
  #colnames(object) <- substr(colnames(object),1,9)
  return(object)

}