## ----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',eval = FALSE, echo=TRUE, message=FALSE, warning=FALSE----
#  maf <- GDCquery_Maf("CHOL", pipelines = "muse")

## ----echo = TRUE, eval = F,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, eval =F, message=FALSE, warning=FALSE----
#  query.maf.hg19 <- GDCquery(project = "TCGA-CHOL",
#                             data.category = "Simple nucleotide variation",
#                             data.type = "Simple somatic mutation",
#                             access = "open",
#                             legacy = TRUE)

## ----echo = TRUE, message = FALSE, eval = F,warning = FALSE--------------
#  # Check maf availables
#  datatable(select(getResults(query.maf.hg19),-contains("cases")),
#            filter = 'top',
#            options = list(scrollX = TRUE, keys = TRUE, pageLength = 10),
#            rownames = FALSE)

## ----results = 'hide', echo=TRUE, eval = F,message=FALSE, warning=FALSE----
#  query.maf.hg19 <- GDCquery(project = "TCGA-CHOL",
#                             data.category = "Simple nucleotide variation",
#                             data.type = "Simple somatic mutation",
#                             access = "open",
#                             file.type = "bcgsc.ca_CHOL.IlluminaHiSeq_DNASeq.1.somatic.maf",
#                             legacy = TRUE)
#  GDCdownload(query.maf.hg19)
#  maf <- GDCprepare(query.maf.hg19)

## ----echo = TRUE, message = FALSE, eval = F, 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,eval = F, warning = FALSE----
#  library(maftools)
#  maf <- GDCquery_Maf("CHOL", pipelines = "muse") %>% read.maf(removeSilent = TRUE, useAll = 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, warning = FALSE, eval = F-------------
#  oncoplot(maf = maf, top = 10, removeNonMutated = TRUE)
#  titv = titv(maf = maf, plot = FALSE, useSyn = TRUE)
#  #plot titv summary
#  plotTiTv(res = titv)