#' Retrieve Significantly Mutated Genes (SMG).
#'
#' 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.
#'
#' @param format Format of result. Default value is json. While json,tsv,csv are available.
#' @param 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.
#' @param 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.
#' @param rank Number of significant genes to return.
#' @param gene Comma separated list of gene name(s). Multiple values are allowed .
#' @param q Only return results with Q-value <= given threshold.
#' @param page Which page (slice) of entire results set should be returned. Multiple values are allowed . Default value is 1.
#' @param page_size Number of records per page of results. Max is 2000. Multiple values are allowed . Default value is 250.
#' @param 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.
#'
#' @export
Analyses.Mutation.SMG = function(format = "json",
cohort = "",
tool = "MutSig2CV",
rank = "",
gene = "",
q = "",
page = "1",
page_size = "250",
sort_by = "rank"
){
parameters = list(format = format,
cohort = cohort,
tool = tool,
rank = rank,
gene = gene,
q = q,
page = page,
page_size = page_size,
sort_by = sort_by)
to.Validate = c("cohort","gene")
validate.Parameters(params = parameters, to.Validate = to.Validate)
url = build.Query(parameters = parameters,
invoker = "Analyses",
method = "Mutation/SMG")
ret = download.Data(url, format, page)
return(ret)
}
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