## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(echo = TRUE)

## ----message=FALSE, warning=FALSE, eval=FALSE---------------------------------
# library(SmCCNet)
# set.seed(123)
# data("ExampleData")
# Y_binary <- ifelse(Y > quantile(Y, 0.5), 1, 0)
# # single-omics PLS
# result <- fastAutoSmCCNet(X = list(X1), Y = as.factor(Y_binary),
#                           Kfold = 3,
#                           subSampNum = 100, DataType = c('Gene'),
#                           saving_dir = tempdir(), EvalMethod = 'auc',
#                           summarization = 'NetSHy',
#                           CutHeight = 1 - 0.1^10, ncomp_pls = 5)
# # single-omics CCA
# result <- fastAutoSmCCNet(X = list(X1), Y = Y, Kfold = 3,
#                           preprocess = FALSE,
#                           subSampNum = 50, DataType = c('Gene'),
#                           saving_dir = tempdir(), summarization = 'NetSHy',
#                           CutHeight = 1 - 0.1^10)
# # multi-omics PLS
# result <- fastAutoSmCCNet(X = list(X1,X2), Y = as.factor(Y_binary),
#                           Kfold = 3, subSampNum = 500,
#                           DataType = c('Gene', 'miRNA'),
#                           CutHeight = 1 - 0.1^10,
#                           saving_dir = tempdir(),
#                           EvalMethod = 'auc',
#                           summarization = 'NetSHy',
#                           BetweenShrinkage = 5,
#                           ncomp_pls = 3, seed = 12345)
# # multi-omics CCA
# result <- fastAutoSmCCNet(X = list(X1,X2), Y = Y,
#                           K = 3, subSampNum = 50,
#                           DataType = c('Gene', 'miRNA'),
#                           CutHeight = 1 - 0.1^10,
#                           saving_dir = tempdir(),
#                           summarization = 'NetSHy',
#                           BetweenShrinkage = 5)