## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = TRUE) knitr::opts_knit$set(progress = FALSE) ## ----message=FALSE, warning=FALSE, include=FALSE------------------------------ library(TCGAbiolinks) library(SummarizedExperiment) library(dplyr) library(DT) ## ----results = 'hide', echo=TRUE, message=FALSE, warning=FALSE,eval=F--------- # query <- GDCquery( # project = "TCGA-CHOL", # data.category = "Simple Nucleotide Variation", # access = "open", # data.type = "Masked Somatic Mutation", # workflow.type = "Aliquot Ensemble Somatic Variant Merging and Masking" # ) # GDCdownload(query) # maf <- GDCprepare(query) ## ----results = 'hide', echo=TRUE, message=FALSE, warning=FALSE,eval=T,include=F---- maf <- chol_maf@data ## ----echo = TRUE, message = FALSE, warning = FALSE---------------------------- # Only first 50 to make render faster datatable(maf[1:20,], filter = 'top', options = list(scrollX = TRUE, keys = TRUE, pageLength = 5), rownames = FALSE) ## ----results = 'hide', echo=TRUE, message=FALSE, warning=FALSE,eval=FALSE----- # maf <- getMC3MAF() ## ----results = "hide",echo = TRUE, message = FALSE, warning = FALSE, eval=FALSE---- # library(maftools) # library(dplyr) # query <- GDCquery( # project = "TCGA-CHOL", # data.category = "Simple Nucleotide Variation", # access = "open", # data.type = "Masked Somatic Mutation", # workflow.type = "Aliquot Ensemble Somatic Variant Merging and Masking" # ) # GDCdownload(query) # maf <- GDCprepare(query) # # maf <- maf %>% maftools::read.maf ## ----message=FALSE, warning=FALSE, include=FALSE------------------------------ library(maftools) library(dplyr) maf <- chol_maf ## ----results = "hide",echo = TRUE, message = FALSE, warning = FALSE----------- datatable(getSampleSummary(maf), filter = 'top', options = list(scrollX = TRUE, keys = TRUE, pageLength = 5), rownames = FALSE) plotmafSummary(maf = maf, rmOutlier = TRUE, addStat = 'median', dashboard = TRUE) ## ----echo = TRUE, message = FALSE,eval = FALSE, warning = FALSE--------------- # oncoplot(maf = maf, top = 10, removeNonMutated = TRUE) # titv = titv(maf = maf, plot = FALSE, useSyn = TRUE) # #plot titv summary # plotTiTv(res = titv)