R/Analyses.CopyNumber.Genes.All.R

In mariodeng/FirebrowseR: An 'API' Client for Broads 'Firehose' Pipeline

#' Retrieve all data by genes Gistic2 results.
#' 
#' This service provides access to the Gistic2 all_data_by_genes.txt output data. This data is a gene-level table of copy number values for all samples. The returned copy number values are in units (copy number - 2) so that no amplification or deletion is 0, genes with amplifications have positive values, and genes with deletions are negative values. The data are converted from marker level to gene level using the extreme method: a gene is assigned the greatest amplification or the least deletion value among the markers it covers. Results may be filtered by cohort, gene, or barcode, but at least one gene or barcode must be supplied.
#'
#' @param format Format of result. Default value is json. While json,tsv,csv are available. 
#' @param cohort Narrow search to one or more TCGA disease cohorts from the scrollable list. Multiple values are allowed ACC,BLCA,BRCA,CESC,CHOL,COAD,COADREAD,DLBC,ESCA,FPPP,GBM,GBMLGG,HNSC,KICH,KIPAN,KIRC,KIRP,LAML,LGG,LIHC,LUAD,LUSC,MESO,OV,PAAD,PCPG,PRAD,READ,SARC,SKCM,STAD,STES,TGCT,THCA,THYM,UCEC,UCS,UVM.
#' @param gene Comma separated list of gene name(s). Multiple values are allowed .
#' @param tcga_participant_barcode Comma separated list of TCGA participant barcodes (e.g. TCGA-GF-A4EO). Multiple values are allowed .
#' @param page Which page (slice) of entire results set should be returned.  Multiple values are allowed . Default value is 1.  
#' @param page_size Number of records per page of results.  Max is 2000. Multiple values are allowed . Default value is 250.  
#' @param sort_by Which column in the results should be used for sorting paginated results? Default value is cohort. While tcga_participant_barcode,cohort,gene are available. 
#' 
#' @export
Analyses.CopyNumber.Genes.All = function(format = "json",
                             cohort = "",
                             gene = "",
                             tcga_participant_barcode = "",
                             page = "1",
                             page_size = "250",
                             sort_by = "cohort"
                             ){
                             
  parameters = list(format = format,
                    cohort = cohort,
                    gene = gene,
                    tcga_participant_barcode = tcga_participant_barcode,
                    page = page,
                    page_size = page_size,
                    sort_by = sort_by)
  to.Validate = c("gene","tcga_participant_barcode")
  validate.Parameters(params = parameters, to.Validate = to.Validate)

  url = build.Query(parameters = parameters,
                    invoker = "Analyses",
                    method = "CopyNumber/Genes/All")
  ret = download.Data(url, format, page)

  return(ret)

}