## ----setup, include = FALSE--------------------------------------------------- is_check <- ("CheckExEnv" %in% search()) || any(c("_R_CHECK_TIMINGS_", "_R_CHECK_LICENSE_") %in% names(Sys.getenv())) knitr::opts_chunk$set(eval = !is_check, collapse = TRUE, comment = "#>") library(ADImpute) ## ----warning=FALSE, message=FALSE, eval=FALSE--------------------------------- # RPM <- NormalizeRPM(ADImpute::demo_data) # imputed <- Impute(data = RPM, do = c("Network"), cores = 2, # net.coef = ADImpute::demo_net) ## ----warning=FALSE, message=FALSE, results=FALSE------------------------------ RPM <- NormalizeRPM(ADImpute::demo_data) methods_pergene <- EvaluateMethods(data = RPM, do = c("Baseline", "DrImpute", "Network"), cores = 2, net.coef = ADImpute::demo_net) ## ----warning=FALSE------------------------------------------------------------ head(methods_pergene) ## ----warning=FALSE, message=FALSE, results=FALSE------------------------------ imputed <- Impute(do = "Ensemble", method.choice = methods_pergene, data = RPM, cores = 2, net.coef = ADImpute::demo_net) ## ----warning=FALSE------------------------------------------------------------ str(imputed) ## ----warning=FALSE, message=FALSE, results=FALSE------------------------------ imputed <- Impute(do = "Baseline", data = RPM, cores = 2, true.zero.thr = .3) ## ----warning=FALSE------------------------------------------------------------ str(imputed) ## ----warning=FALSE, message=FALSE, results=FALSE------------------------------ sce <- NormalizeRPM(sce = ADImpute::demo_sce) sce <- EvaluateMethods(sce = sce) sce <- Impute(sce = sce) ## ----warning=FALSE, eval=FALSE------------------------------------------------ # # # call to scImpute # if('scimpute' %in% tolower(do)){ # message('Make sure you have previously installed scImpute via GitHub.\n') # res <- tryCatch(ImputeScImpute(count_path, labeled = is.null(labels), # Kcluster = cell.clusters, labels = labels, drop_thre = drop_thre, # cores = cores, type = type, tr.length = tr.length), # error = function(e){ stop(paste('Error:', e$message, # '\nTry sourcing the Impute_extra.R file.'))}) # imputed$scImpute <- log2( (res / scale) + pseudo.count) # } # # # call to SCRABBLE # if('scrabble' %in% tolower(do)){ # message('Make sure you have previously installed SCRABBLE via GitHub.\n') # res <- tryCatch(ImputeSCRABBLE(data, bulk), # error = function(e) { stop(paste('Error:', e$message, # '\nTry sourcing the Impute_extra.R file.'))}) # imputed$SCRABBLE <- log2( (res / scale) + pseudo.count) # rm(res);gc() # } ## ----------------------------------------------------------------------------- sessionInfo()