## ----inf1, echo=FALSE, message=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')$betas # model <- sesameAnno_get("Anno/HM450/Clock_Horvath353.rds") # predictAge(betas, model) ## ----inf18, message=FALSE, eval=FALSE----------------------------------------- # library(SummarizedExperiment) # betas <- assay(sesameDataGet("MM285.10.SE.tissue"))[,1] # model <- sesameAnno_get("Anno/MM285/Clock_Zhou347.rds") # predictAge(betas, model) ## ----inf20, echo=FALSE, result="asis"----------------------------------------- library(knitr) df <- data.frame(rbind( c("Anno/HM450/Clock_Horvath353.rds", 353, "HM450/EPIC", "Horvath 2013 (24138928)"), c("Anno/HM450/Clock_Hannum.rds", 71, "HM450", "Hannum 2013 (23177740)"), c("Anno/HM450/Clock_SkinBlood.rds", 391, "HM450/EPIC", "Horath 2018 (30048243)"), c("Anno/EPIC/Clock_PhenoAge.rds", 514, "HM450/EPIC", "Levine 2018 (29676998)"), c("Anno/MM285/Clock_Zhou347.rds", 347, "MM285", "Zhou 2022") )) colnames(df) <- c("RDS Key", "Platform", "N", "Reference (PMID)") kable(df, caption="Available Epigenetic Clocks") ## ----inf7, message=FALSE------------------------------------------------------ betas.tissue <- sesameDataGet('HM450.1.TCGA.PAAD')$betas estimateLeukocyte(betas.tissue) ## ----inf8, message=FALSE, warning=FALSE, include=FALSE------------------------ library(sesame) sesameDataCacheAll() ## ----inf9, eval=FALSE--------------------------------------------------------- # tmp = tempdir() # res_grn = sesameAnno_download("Test/3999492009_R01C01_Grn.idat", dest_dir=tmp) # res_red = sesameAnno_download("Test/3999492009_R01C01_Red.idat", dest_dir=tmp) ## ----inf10, eval=FALSE-------------------------------------------------------- # # deIdentify(res_grn$dest_file, sprintf("%s/deidentified_Grn.idat", tmp)) # deIdentify(res_red$dest_file, sprintf("%s/deidentified_Red.idat", tmp)) # # betas1 = getBetas(readIDATpair(sprintf("%s/Test/3999492009_R01C01", tmp))) # betas2 = getBetas(readIDATpair(sprintf("%s/deidentified", tmp))) # # head(betas1[grep('rs',names(betas1))]) # head(betas2[grep('rs',names(betas2))]) ## ----inf11, eval=FALSE-------------------------------------------------------- # # my_secret <- 13412084 # set.seed(my_secret) # # deIdentify(res_grn$dest_file, # sprintf("%s/deidentified_Grn.idat", tmp), randomize=TRUE) # # my_secret <- 13412084 # set.seed(my_secret) # deIdentify(res_red$dest_file, # sprintf("%s/deidentified_Red.idat", tmp), randomize=TRUE) # # betas1 = getBetas(readIDATpair(sprintf("%s/Test/3999492009_R01C01", tmp))) # betas2 = getBetas(readIDATpair(sprintf("%s/deidentified", tmp))) # # 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(sprintf("%s/deidentified_Red.idat", tmp), # sprintf("%s/reidentified_Red.idat", tmp)) # # betas1 = getBetas(readIDATpair(sprintf("%s/Test/3999492009_R01C01", tmp))) # betas2 = getBetas(readIDATpair(sprintf("%s/reidentified", tmp))) # # head(betas1[grep('rs',names(betas1))]) # head(betas2[grep('rs',names(betas2))]) ## ----------------------------------------------------------------------------- sessionInfo()