## ----设置，包括= false -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------（“ checkexenv”％in％search（））||任何（c（“ _ r_check_timings_”，“ _r_check_license_”）％in％names（sys.getenv（）））knitr :: opts_chunk $ set $ set（eval =！is_check，collapse，collapse = true = true，true，comment =“ primpl =”＃>“＃”）图书馆（atimpe）## ----警告= false，message = false，eval = false ---------------------------------------------------------------------------------------------------------------------＃rpm <-SustranizerPm（atimptute :: demo_data）＃插入< - 插入（data = rpm，do = c（“ network”），cores = 2，＃net.coef = adimptute :: demo_net）## -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------warning=FALSE, message=FALSE, results=FALSE----------------------------- RPM <- NormalizeRPM(ADImpute::demo_data)methods_pergene < - evaluateMethods（data = rpm，do = c（“基线”，“ drimpute”，“ network”），cores = 2，net.coef = adimptute :: demo_net）## ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- head（methots_pergene）## ----警告= false，message = false，结果= false ----------------------------------------------------------------------------------------------估算< - 插入（do =“集合”，method.choice = methods_pergene，data = rpm，cores = 2，net.coef = adimptute :: demo_net）## ----警告= false = 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()