Archives.StandardData: Retrieve standard data archives.

Description Usage Arguments

View source: R/Archives.StandardData.R

Description

This service returns the archive URLs for our Firehose standard data runs, providing a RESTful interface similar in spirit to the command line <a href="https://confluence.broadinstitute.org/display/GDAC/Download">firehose_get</a> tool. The archives can be filtered based on date, cohort, data type, platform, center, data level, and protocol.

Usage

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Archives.StandardData(format = "json", date = "2016_01_28", cohort = "",
  data_type = "", tool = "", platform = "", center = "", level = "",
  protocol = "", page = "1", page_size = "250", 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.

data_type

Narrow search to one or more TCGA data types from the scrollable list. Multiple values are allowed Clinical,CopyNumber,LowPass,MAF,Methylation,miR,miRSeq,mRNA,mRNASeq,rawMAF,rawWIG,RPPA,WIG.

tool

Narrow search to include only data/results produced by the selected Firehose tool. Multiple values are allowed Clinical_Pick_Tier1,Merge_Clinical,Merge_cna__cgh_1x1m_g4447a__mskcc_org__Level_3__segmentation_data_computation__seg,Merge_cna__hg_cgh_244a__hms_harvard_edu__Level_3__segmentation__seg,Merge_cna__hg_cgh_244a__mskcc_org__Level_3__segmentation_data_computation__seg,Merge_cna__hg_cgh_415k_g4124a__hms_harvard_edu__Level_3__segmentation__seg,Merge_cna__illuminahiseq_dnaseqc__hms_harvard_edu__Level_3__segmentation__seg,Merge_exon__huex_1_0_st_v2__lbl_gov__Level_2__quantile_normalization_exon__data,Merge_exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data,Merge_exon__huex_1_0_st_v2__lbl_gov__Level_3__segmented_as_firma__data,Merge_methylation__humanmethylation27__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data,Merge_methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data,Merge_mirna__h_mirna_8x15k__unc_edu__Level_3__unc_DWD_Batch_adjusted__data,Merge_mirna__h_mirna_8x15kv2__unc_edu__Level_3__unc_DWD_Batch_adjusted__data,Merge_mirnaseq__illuminaga_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data,Merge_mirnaseq__illuminaga_mirnaseq__bcgsc_ca__Level_3__miR_isoform_expression__data,Merge_mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data,Merge_mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_isoform_expression__data,Merge_protein_exp__mda_rppa_core__mdanderson_org__Level_3__protein_normalization__data,Merge_rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__exon_expression__data,Merge_rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__gene_expression__data,Merge_rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__splice_junction_expression__data,Merge_rnaseq__illuminaga_rnaseq__unc_edu__Level_3__exon_expression__data,Merge_rnaseq__illuminaga_rnaseq__unc_edu__Level_3__gene_expression__data,Merge_rnaseq__illuminaga_rnaseq__unc_edu__Level_3__splice_junction_expression__data,Merge_rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__exon_expression__data,Merge_rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__gene_expression__data,Merge_rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__splice_junction_expression__data,Merge_rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__exon_expression__data,Merge_rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__gene_expression__data,Merge_rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__splice_junction_expression__data,Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__exon_quantification__data,Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__junction_quantification__data,Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__RSEM_genes__data,Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data,Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__RSEM_isoforms__data,Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__RSEM_isoforms_normalized__data,Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__exon_quantification__data,Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__junction_quantification__data,Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data,Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data,Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_isoforms__data,Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_isoforms_normalized__data,Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_2__birdseed_genotype__birdseed,Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg18__seg,Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg19__seg,Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg18__seg,Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg,Merge_snp__human1mduo__hudsonalpha_org__Level_3__segmented_cna__seg,Merge_snp__human1mduo__hudsonalpha_org__Level_3__segmented_cnv__seg,Merge_snp__human1mduo__hudsonalpha_org__Level_3__segmented_loh__seg,Merge_snp__humanhap550__hudsonalpha_org__Level_3__segmented_cna__seg,Merge_snp__humanhap550__hudsonalpha_org__Level_3__segmented_cnv__seg,Merge_snp__humanhap550__hudsonalpha_org__Level_3__segmented_loh__seg,Merge_transcriptome__agilentg4502a_07_1__unc_edu__Level_2__unc_lowess_normalization_probe_level__data,Merge_transcriptome__agilentg4502a_07_1__unc_edu__Level_3__unc_lowess_normalization_gene_level__data,Merge_transcriptome__agilentg4502a_07_2__unc_edu__Level_2__unc_lowess_normalization_probe_level__data,Merge_transcriptome__agilentg4502a_07_2__unc_edu__Level_3__unc_lowess_normalization_gene_level__data,Merge_transcriptome__agilentg4502a_07_3__unc_edu__Level_2__unc_lowess_normalization_probe_level__data,Merge_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data,Merge_transcriptome__ht_hg_u133a__broad_mit_edu__Level_2__probeset_rma__data,Merge_transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data,Methylation_Preprocess,miRseq_Mature_Preprocess,miRseq_Preprocess,mRNA_Preprocess_Median,mRNAseq_Preprocess,Mutation_Packager_Calls,Mutation_Packager_Coverage,Mutation_Packager_Oncotated_Calls,Mutation_Packager_Oncotated_Raw_Calls,Mutation_Packager_Raw_Calls,Mutation_Packager_Raw_Coverage,RPPA_AnnotateWithGene.

platform

Narrow search to one or more TCGA data generation platforms from the scrollable list. Multiple values are allowed 454,ABI,AgilentG4502A_07,AgilentG4502A_07_1,AgilentG4502A_07_2,AgilentG4502A_07_3,bio,biotab,CGH-1x1M_G4447A,diagnostic_images,fh_analyses,fh_reports,fh_stddata,Genome_Wide_SNP_6,GenomeWideSNP_5,H-miRNA_8x15K,H-miRNA_8x15Kv2,H-miRNA_EarlyAccess,H-miRNA_G4470A,HG-CGH-244A,HG-CGH-415K_G4124A,HG-U133_Plus_2,HG-U133A_2,HT_HG-U133A,HuEx-1_0-st-v2,Human1MDuo,HumanHap550,HumanMethylation27,HumanMethylation450,IlluminaDNAMethylation_OMA002_CPI,IlluminaDNAMethylation_OMA003_CPI,IlluminaGA_DNASeq,IlluminaGA_DNASeq_automated,IlluminaGA_DNASeq_Cont,IlluminaGA_DNASeq_Cont_automated,IlluminaGA_DNASeq_Cont_curated,IlluminaGA_DNASeq_curated,IlluminaGA_miRNASeq,IlluminaGA_mRNA_DGE,IlluminaGA_RNASeq,IlluminaGA_RNASeqV2,IlluminaGG,IlluminaHiSeq_DNASeq,IlluminaHiSeq_DNASeq_automated,IlluminaHiSeq_DNASeq_Cont,IlluminaHiSeq_DNASeq_Cont_automated,IlluminaHiSeq_DNASeq_Cont_curated,IlluminaHiSeq_DNASeq_curated,IlluminaHiSeq_DNASeqC,IlluminaHiSeq_miRNASeq,IlluminaHiSeq_mRNA_DGE,IlluminaHiSeq_RNASeq,IlluminaHiSeq_RNASeqV2,IlluminaHiSeq_TotalRNASeqV2,IlluminaHiSeq_WGBS,Mapping250K_Nsp,Mapping250K_Sty,MDA_RPPA_Core,microsat_i,minbio,minbiotab,Mixed_DNASeq,Mixed_DNASeq_automated,Mixed_DNASeq_Cont,Mixed_DNASeq_Cont_automated,Mixed_DNASeq_Cont_curated,Mixed_DNASeq_curated,pathology_reports,SOLiD_DNASeq,SOLiD_DNASeq_automated,SOLiD_DNASeq_Cont,SOLiD_DNASeq_Cont_automated,SOLiD_DNASeq_Cont_curated,SOLiD_DNASeq_curated,tissue_images,WHG-1x44K_G4112A,WHG-4x44K_G4112F,WHG-CGH_4x44B.

center

Narrow search to one or more TCGA centers from the scrollable list. Multiple values are allowed bcgsc.ca,broad.mit.edu,broadinstitute.org,genome.wustl.edu,hgsc.bcm.edu,hms.harvard.edu,hudsonalpha.org,intgen.org,jhu-usc.edu,jhu.edu,lbl.gov,mdanderson.org,mskcc.org,nationwidechildrens.org,pnl.gov,rubicongenomics.com,sanger.ac.uk,systemsbiology.org,ucsc.edu,unc.edu,vanderbilt.edu.

level

Narrow search to one or more TCGA data levels. Multiple values are allowed 1,2,3,4.

protocol

Narrow search to one or more sample characterization protocols from the scrollable list. Multiple values are allowed birdseed_genotype,exon_expression,exon_quantification,gene_expression,gene_rma,junction_quantification,miR_gene_expression,miR_isoform_expression,probeset_rma,protein_normalization,quantile_normalization_exon,quantile_normalization_gene,RSEM_genes,RSEM_genes_normalized,RSEM_isoforms,RSEM_isoforms_normalized,segmentation,segmentation_data_computation,segmented_as_firma,segmented_cna,segmented_cnv,segmented_loh,segmented_scna_hg18,segmented_scna_hg19,segmented_scna_minus_germline_cnv_hg18,segmented_scna_minus_germline_cnv_hg19,splice_junction_expression,unc_DWD_Batch_adjusted,unc_lowess_normalization_gene_level,unc_lowess_normalization_probe_level,within_bioassay_data_set_function.

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 cohort,protocol,center,data_type,level,tool,platform,date are available.


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