Analyses.Reports: Retrieve links to summary reports from Firehose analysis...

Description Usage Arguments

View source: R/Analyses.Reports.R

Description

This service returns URLs to the analysis result reports for runs of the Broad Institute GDAC Firehose analysis pipeline. At least one year of run reports are maintained in the database, but the reports from the latest run will be returned by default. The set of <a href="https://confluence.broadinstitute.org/display/GDAC/Nozzle">Nozzle</a> reports returned may be filtered by disease cohort, report type and report name.

Usage

1
2
3
Analyses.Reports(format = "json", date = "2016_01_28", cohort = "",
  name = "", type = "", page = "1", page_size = "250",
  sort_by = "date")

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_08_21,2015_04_02,2014_10_17,2014_07_15,2014_04_16,2014_01_15,2013_09_23,2013_05_23,2013_04_21. 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.

name

Narrow search to one or more report names. Multiple values are allowed Aggregate_AnalysisFeatures,CopyNumber_Clustering_CNMF,CopyNumber_Clustering_CNMF_thresholded,CopyNumber_Gistic2,CopyNumberLowPass_Gistic2,Correlate_Clinical_vs_CopyNumber_Arm,Correlate_Clinical_vs_CopyNumber_Focal,Correlate_Clinical_vs_Methylation,Correlate_Clinical_vs_miR,Correlate_Clinical_vs_miRseq,Correlate_Clinical_vs_Molecular_Subtypes,Correlate_Clinical_vs_mRNA,Correlate_Clinical_vs_mRNAseq,Correlate_Clinical_vs_Mutation,Correlate_Clinical_vs_Mutation_APOBEC_Categorical,Correlate_Clinical_vs_Mutation_APOBEC_Continuous,Correlate_Clinical_vs_MutationRate,Correlate_Clinical_vs_RPPA,Correlate_CopyNumber_vs_miR,Correlate_CopyNumber_vs_mRNA,Correlate_CopyNumber_vs_mRNAseq,Correlate_Methylation_vs_mRNA,Correlate_molecularSubtype_vs_CopyNumber_Arm,Correlate_molecularSubtype_vs_CopyNumber_Focal,Correlate_molecularSubtype_vs_Mutation,Correlate_mRNAseq_vs_Mutation_APOBEC,Methylation_Clustering_CNMF,miR_Clustering_CNMF,miR_Clustering_Consensus,miR_Clustering_Consensus_Plus,miR_FindDirectTargets,miRseq_Clustering_CNMF,miRseq_Clustering_Consensus,miRseq_Clustering_Consensus_Plus,miRseq_FindDirectTargets,miRseq_Mature_Clustering_CNMF,miRseq_Mature_Clustering_Consensus,miRseq_Mature_Clustering_Consensus_Plus,mRNA_Clustering_CNMF,mRNA_Clustering_Consensus,mRNA_Clustering_Consensus_Plus,mRNAseq_Clustering_CNMF,mRNAseq_Clustering_Consensus,mRNAseq_Clustering_Consensus_Plus,Mutation_APOBEC,Mutation_Assessor,Mutation_CHASM,MutSig2.0,MutSig2CV,MutSigCV,MutSigNozzleReport1.5,MutSigNozzleReport2.0,MutSigNozzleReport2CV,MutSigNozzleReportCV,MutSigNozzleReportMerged,Pathway_FindEnrichedGenes,Pathway_GSEA_mRNAseq,Pathway_Hotnet,Pathway_Overlaps_MSigDB_MutSig2CV,Pathway_Paradigm_mRNA,Pathway_Paradigm_mRNA_And_Copy_Number,Pathway_Paradigm_RNASeq,Pathway_Paradigm_RNASeq_And_Copy_Number,RPPA_Clustering_CNMF,RPPA_Clustering_Consensus,RPPA_Clustering_Consensus_Plus.

type

Narrow search to one or more report types. Multiple values are allowed Aggregate,Clustering,CopyNumber,Correlations,Expression,Mutation,Pathway.

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 date. While date,cohort,type,name are available.


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