Analyses.mRNASeq.Quartiles: Returns RNASeq expression quartiles, e.g. suitable for...

Description Usage Arguments

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

Description

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.

Usage

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

Arguments

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 .


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