From 8500696ebd4b8d677c3b994e130eada766cdec4b Mon Sep 17 00:00:00 2001 From: LiNk-NY Date: Sat, 3 Aug 2019 23:52:33 -0400 Subject: [PATCH] update RTCGAToolbox code --- vignettes/TCGAWorkflowData.Rmd | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/vignettes/TCGAWorkflowData.Rmd b/vignettes/TCGAWorkflowData.Rmd index 8f3703d..edca245 100644 --- a/vignettes/TCGAWorkflowData.Rmd +++ b/vignettes/TCGAWorkflowData.Rmd @@ -68,12 +68,12 @@ Download and save a subset of GBM GISTIC results from GDAC firehose. library(RTCGAToolbox) # Download GISTIC results lastAnalyseDate <- getFirehoseAnalyzeDates(1) -gistic <- getFirehoseData("GBM",gistic2_Date = lastAnalyseDate) +gistic <- getFirehoseData("GBM", gistic2Date = lastAnalyseDate, GISTIC = TRUE) # get GISTIC results -gistic.allbygene <- getData(gistic,type = "GISTIC", CN = "All") +gistic.allbygene <- getData(gistic,type = "GISTIC", platform = "AllByGene") gistic.allbygene <- gistic.allbygene[1:10,] -gistic.thresholedbygene <- getData(gistic,type = "GISTIC", CN = "Thresholed") +gistic.thresholedbygene <- getData(gistic,type = "GISTIC", platform = "ThresholdedByGene") gistic.thresholedbygene <- gistic.thresholedbygene[1:10,] save(gistic.allbygene,gistic.thresholedbygene,file = "GBMGistic.rda", compress = "xz") ```