## ----inf1, echo=FALSE, message=FALSE, warning=FALSE---------------------------
library(sesame)
sesameDataCache()
sdf = sesameDataGet('EPIC.1.SigDF')

## ----inf2, message=FALSE------------------------------------------------------
sdf = sesameDataGet('EPIC.1.SigDF')
inferSex(sdf)
inferSexKaryotypes(sdf)

## ----nh16, message=FALSE------------------------------------------------------
sdf = sesameDataGet("MM285.1.SigDF")
inferSex(sdf)

## ----inf3---------------------------------------------------------------------
sdf = sesameDataGet('EPIC.1.SigDF')
inferEthnicity(sdf)

## ----inf4, eval=FALSE---------------------------------------------------------
#  betas <- sesameDataGet('HM450.1.TCGA.PAAD')$betas
#  ## download clock file from http://zwdzwd.github.io/InfiniumAnnotation
#  model <- readRDS("~/Downloads/Clock_Horvath353.rds")
#  predictAge(betas, model)

## ----inf18, message=FALSE, eval=FALSE-----------------------------------------
#  library(SummarizedExperiment)
#  betas <- assay(sesameDataGet("MM285.10.SE.tissue"))[,1]
#  ## download clock file from http://zwdzwd.github.io/InfiniumAnnotation
#  model <- readRDS("~/Downloads/Clock_Zhou347.rds")
#  predictAge(betas, model)

## ----inf7, message=FALSE------------------------------------------------------
betas.tissue <- sesameDataGet('HM450.1.TCGA.PAAD')$betas
estimateLeukocyte(betas.tissue)

## ----inf8, message=FALSE, warning=FALSE, include=FALSE------------------------
library(sesame)
sesameDataCacheAll()

## ----inf10, eval=FALSE--------------------------------------------------------
#  
#  deIdentify("~/Downloads/3999492009_R01C01_Grn.idat",
#      "~/Downloads/deidentified_Grn.idat")
#  deIdentify("~/Downloads/3999492009_R01C01_Red.idat",
#      "~/Downloads/deidentified_Red.idat")
#  
#  betas1 = getBetas(readIDATpair("~/Downloads/3999492009_R01C01"))
#  betas2 = getBetas(readIDATpair("~/Downloads/deidentified"))
#  
#  head(betas1[grep('rs',names(betas1))])
#  head(betas2[grep('rs',names(betas2))])

## ----inf11, eval=FALSE--------------------------------------------------------
#  
#  my_secret <- 13412084
#  set.seed(my_secret)
#  
#  deIdentify("~/Downloads/3999492009_R01C01_Grn.idat",
#      "~/Downloads/deidentified_Grn.idat", randomize=TRUE)
#  
#  my_secret <- 13412084
#  set.seed(my_secret)
#  deIdentify("~/Downloads/3999492009_R01C01_Red.idat",
#      "~/Downloads/deidentified_Red.idat", randomize=TRUE)
#  
#  betas1 = getBetas(readIDATpair("~/Downloads/3999492009_R01C01"))
#  betas2 = getBetas(readIDATpair("~/Downloads/deidentified"))
#  
#  head(betas1[grep('rs',names(betas1))])
#  head(betas2[grep('rs',names(betas2))])
#  

## ----inf12, eval=FALSE--------------------------------------------------------
#  
#  my_secret <- 13412084
#  set.seed(my_secret)
#  
#  reIdentify(sprintf("%s/deidentified_Grn.idat", tmp),
#      sprintf("%s/reidentified_Grn.idat", tmp))
#  
#  my_secret <- 13412084
#  set.seed(my_secret)
#  reIdentify("~/Downloads/deidentified_Red.idat",
#      "~/Downloads/reidentified_Red.idat")
#  
#  betas1 = getBetas(readIDATpair("~/Downloads/3999492009_R01C01"))
#  betas2 = getBetas(readIDATpair("~/Downloads/reidentified"))
#  
#  head(betas1[grep('rs',names(betas1))])
#  head(betas2[grep('rs',names(betas2))])

## -----------------------------------------------------------------------------
sessionInfo()

