## ----install, warning=FALSE, message=FALSE, eval=FALSE--------------------- # if (!requireNamespace("BiocManager")) # install.packages("BiocManager") # BiocManager::install("pwrEWAS") ## ----library, warning=FALSE, message=FALSE, eval=TRUE---------------------- library("pwrEWAS") ## ----usage, warning=FALSE, message=FALSE, eval=TRUE, results="hide"-------- # providing the targeted maximal difference in DNAm results_targetDelta <- pwrEWAS(minTotSampleSize = 10, maxTotSampleSize = 50, SampleSizeSteps = 10, NcntPer = 0.5, targetDelta = c(0.2, 0.5), J = 100, targetDmCpGs = 10, tissueType = "Adult (PBMC)", detectionLimit = 0.01, DMmethod = "limma", FDRcritVal = 0.05, core = 4, sims = 50) # providing the targeted maximal difference in DNAm results_deltaSD <- pwrEWAS(minTotSampleSize = 10, maxTotSampleSize = 50, SampleSizeSteps = 10, NcntPer = 0.5, deltaSD = c(0.02, 0.05), J = 100, targetDmCpGs = 10, tissueType = "Adult (PBMC)", detectionLimit = 0.01, DMmethod = "limma", FDRcritVal = 0.05, core = 4, sims = 50) ## ----example running pwrEWAS targetDelta, warning=FALSE, message=FALSE, eval=FALSE, results="hide"---- # library(pwrEWAS) # set.seed(1234) # results_targetDelta <- pwrEWAS(minTotSampleSize = 20, # maxTotSampleSize = 260, # SampleSizeSteps = 40, # NcntPer = 0.5, # targetDelta = c(0.02, 0.10, 0.15, 0.20), # J = 100000, # targetDmCpGs = 2500, # tissueType = "Blood adult", # detectionLimit = 0.01, # DMmethod = "limma", # FDRcritVal = 0.05, # core = 4, # sims = 50) # # results_deltaSD <- pwrEWAS(minTotSampleSize = 20, # maxTotSampleSize = 260, # SampleSizeSteps = 40, # NcntPer = 0.5, # deltaSD = c(0.00390625, 0.02734375, 0.0390625, 0.052734375), # J = 100000, # targetDmCpGs = 2500, # tissueType = "Blood adult", # detectionLimit = 0.01, # DMmethod = "limma", # FDRcritVal = 0.05, # core = 4, # sims = 50) # ## ----echo=FALSE, results='hide',message=FALSE------------------------------ load("vignette_reduced.Rdata") ## ----example running pwrEWAS targetDelta time stamps, warning=FALSE, message=FALSE, eval=TRUE---- ## [2019-02-12 18:40:23] Finding tau...done [2019-02-12 18:42:53] ## [1] "The following taus were chosen: 0.00390625, 0.02734375, 0.0390625, 0.052734375" ## [2019-02-12 18:42:53] Running simulation ## |===================================================================| 100% ## [2019-02-12 18:42:53] Running simulation ... done [2019-02-12 19:27:03] ## ----example results_targetDelta str, warning=FALSE, message=FALSE, eval=TRUE---- attributes(results_targetDelta) ## $names ## [1] "meanPower" "powerArray" "deltaArray" "metric" ## ----example results_targetDeltaput mean power, warning=FALSE, message=FALSE, eval=TRUE---- dim(results_targetDelta$meanPower) print(results_targetDelta$meanPower) ## ----example power plot, warning=FALSE, message=FALSE, eval=TRUE----------- dim(results_targetDelta$powerArray) # simulations x sample sizes x effect sizes pwrEWAS_powerPlot(results_targetDelta$powerArray, sd = FALSE) ## ----example max delta, warning=FALSE, message=FALSE, eval=FALSE----------- # # maximum value of simulated differences by target value # lapply(results_targetDelta$deltaArray, max) # ## $`0.02` # ## [1] 0.02095302 # ## # ## $`0.1` # ## [1] 0.1265494 # ## # ## $`0.15` # ## [1] 0.2045638 # ## # ## $`0.2` # ## [1] 0.2458416 # # # percentage of simulated differences to be within the target range # mean(results _ targetDelta$deltaArray[[1]] < 0.02) # ## [1] 0.9999999 # mean(results _ targetDelta$deltaArray[[2]] < 0.10) # ## [1] 0.9998882 # mean(results _ targetDelta$deltaArray[[3]] < 0.15) # ## [1] 0.9999386 # mean(results _ targetDelta$deltaArray[[4]] < 0.20) # ## [1] 0.9999539 ## ----example density plot, warning=FALSE, message=FALSE, eval=FALSE-------- # pwrEWAS_deltaDensity(results_targetDelta$deltaArray, detectionLimit = 0.01, sd = FALSE) ## ----example density plot w/o 0.02, warning=FALSE, message=FALSE, eval=FALSE---- # temp <- results_targetDelta$deltaArray # temp[[1]] <- NULL # pwrEWAS_deltaDensity(temp, detectionLimit = 0.01, sd = FALSE) ## ----example metrics, warning=FALSE, message=FALSE, eval=TRUE-------------- results_targetDelta$metric ## ----sessionInfo, results='asis', echo=TRUE-------------------------------- toLatex(sessionInfo())