Analyses.mRNASeq.Quartiles: Returns RNASeq expression quartiles, e.g. suitable for...
In mariodeng/FirebrowseR: An 'API' Client for Broads 'Firehose' Pipeline

View source: R/Analyses.mRNASeq.Quartiles.R

For a given gene compute quartiles and extrema, suitable e.g. for drawing a boxplot (Tukey 1977). Results may be filtered by cohort, sample type, patient barcode or characterization protocol, and are returned sorted by cohort. Note that samples for which no expression value was recorded (e.g. <a href="http://firebrowse.org/api/v1/Samples/mRNASeq?&gene=egfr&cohort=SKCM&tcga_participant_barcode=TCGA-GN-A262">the melanoma sample TCGA-GN-262</a>) are removed prior to calculation.

1 2	Analyses.mRNASeq.Quartiles(format = "json", gene = "", cohort = "", protocol = "RSEM", sample_type = "tumors", Exclude = "")

`format`	Format of result. Default value is json. While json,tsv,csv are available.
`gene`	Enter a single gene name.
`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.
`protocol`	Narrow search to one or more sample characterization protocols from the scrollable list. Multiple values are allowed RPKM,RSEM. Default value is RSEM.
`sample_type`	For which type of sample(s) should quartiles be computed? Multiple values are allowed tumors,normals,TP,TB,TAM,TBM,NBC,TRB,TR,TRBM,TAP,TM,THOC,NB,NT,NEBV,NBM. Default value is tumors.
`Exclude`	Comma separated list of TCGA participants, identified by barcodes such as TCGA-GF-A4EO, denoting samples to exclude from computation. Multiple values are allowed .