Analyses.CopyNumber.Genes.Thresholded: Retrieve all thresholded by genes Gistic2 results.

Description Usage Arguments

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

Description

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.

Usage

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

Arguments

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.


mariodeng/FirebrowseR documentation built on May 21, 2017, 6:48 p.m.