## ----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()