Metadata.Counts: Retrieve sample counts.

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

Description

Returns the aliquot counts for each disease cohort, per sample type and data type. The sample type designation of "Tumor" may be used to aggregate the count of all tumor aliquots into a single number per disease and data type. See the SampleTypes function for a complete description of sample types.

Usage

Metadata.Counts(format = "json", date = "2016_01_28", cohort = "",
  sample_type = "", data_type = "", totals = "TRUE", sort_by = "cohort")

Arguments

format	Format of result. Default value is json. While json,tsv,csv are available.
date	Select one or more date stamps. Multiple values are allowed 2016_01_28,2015_11_01,2015_08_21,2015_06_01,2015_04_02,2015_02_04,2014_12_06,2014_10_17,2014_09_02,2014_07_15,2014_05_18,2014_04_16,2014_03_16. Default value is 2016_01_28.
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.
sample_type	Narrow search to one or more TCGA sample types from the scrollable list. Multiple values are allowed FFPE,NB,NBC,NBM,NT,TAM,TAP,TB,TM,TP,TR,Tumor.
data_type	Narrow search to one or more TCGA data types from the scrollable list. Multiple values are allowed bcr,clinical,cn,lowp,methylation,mrna,mrnaseq,mir,mirseq,rppa,maf,rawmaf.
totals	Output an entry providing the totals for each data type. Default value is TRUE. While are available.
sort_by	Which column in the results should be used for sorting paginated results? Default value is cohort. While cohort are available.

mariodeng/FirebrowseR documentation built on May 21, 2019, 11:46 a.m.