Samples.mRNASeq: Retrieve mRNASeq data.

Description Usage Arguments

View source: R/Samples.mRNASeq.R

Description

This service returns sample-level log2 mRNASeq expression values. Results may be filtered by gene, cohort, barcode, sample type or characterization protocol, but at least one gene must be supplied.

Usage

1
2
3
Samples.mRNASeq(format = "json", gene = "", cohort = "",
  tcga_participant_barcode = "", sample_type = "", protocol = "RSEM",
  page = "1", page_size = "250", sort_by = "cohort")

Arguments

format

Format of result. Default value is json. While json,tsv,csv are available.

gene

Comma separated list of gene name(s). Multiple values are allowed .

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.

tcga_participant_barcode

Comma separated list of TCGA participant barcodes (e.g. TCGA-GF-A4EO). Multiple values are allowed .

sample_type

Narrow search to one or more TCGA sample types from the scrollable list. Multiple values are allowed NB,NBC,NBM,NT,TAM,TAP,TB,TM,TP,TR.

protocol

Narrow search to one or more sample characterization protocols from the scrollable list. Multiple values are allowed RPKM,RSEM. Default value is RSEM.

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,protocol,sample_type are available.


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