## ----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()

