Analyses.Mutation.SMG: Retrieve Significantly Mutated Genes (SMG).

Description Usage Arguments

View source: R/Analyses.Mutation.SMG.R

Description

This service provides a list of significantly mutated genes, as scored by MutSig. It may be filtered by cohort, rank, gene, tool and/or Q-value threshold, but at least one cohort or gene must be supplied.

Usage

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Analyses.Mutation.SMG(format = "json", cohort = "", tool = "MutSig2CV",
  rank = "", gene = "", q = "", page = "1", page_size = "250",
  sort_by = "rank")

Arguments

format

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

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.

tool

Narrow search to include only data/results produced by the selected Firehose tool. Multiple values are allowed MutSig2.0,MutSig2CV,MutSigCV. Default value is MutSig2CV.

rank

Number of significant genes to return.

gene

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

q

Only return results with Q-value <= given threshold.

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 rank. While q,cohort,tool,gene,rank are available.


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