Analyses.CopyNumber.Genes.Thresholded: Retrieve all thresholded by genes Gistic2 results.
In mariodeng/FirebrowseR: An 'API' Client for Broads 'Firehose' Pipeline

View source: R/Analyses.CopyNumber.Genes.Thresholded.R

This service provides access to the Gistic2 all_thresholded_by_genes.txt output data. A gene-level table of discrete amplification and deletion indicators for all samples. A table value of 0 means no amplification or deletion above the threshold. Amplifications are positive numbers: 1 means amplification above the amplification threshold; 2 means amplifications larger to the arm level amplifications observed for the sample. Deletions are represented by negative table values: -1 represents deletion beyond the threshold; -2 means deletions greater than the minimum arm-level deletion observed for the sample. Results maybe filtered by cohort, gene or barcode, but at least one gene or barcode must be supplied.

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Analyses.CopyNumber.Genes.Thresholded(format = "json", cohort = "",
  gene = "", tcga_participant_barcode = "", page = "1",
  page_size = "250", sort_by = "cohort")

`format`	Format of result. Default value is json. While json,tsv,csv are available.
`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.
`gene`	Comma separated list of gene name(s). Multiple values are allowed .
`tcga_participant_barcode`	Comma separated list of TCGA participant barcodes (e.g. TCGA-GF-A4EO). Multiple values are allowed .
`page`	Which page (slice) of entire results set should be returned. Multiple values are allowed . Default value is 1.
`page_size`	Number of records per page of results. Max is 2000. Multiple values are allowed . Default value is 250.
`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.