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## ----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 = getwd(), 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 = getwd(), summarization = 'NetSHy',
# CutHeight = 1 - 0.1^10)
# # multi-omics PLS
# result <- fastAutoSmCCNet(X = list(X1,X2), Y = as.factor(Y_binary),
# Kfold = 3, subSampNum = 50,
# DataType = c('Gene', 'miRNA'),
# CutHeight = 1 - 0.1^10,
# saving_dir = getwd(),
# EvalMethod = 'auc',
# summarization = 'NetSHy',
# BetweenShrinkage = 5,
# ncomp_pls = 3)
# # 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 = getwd(),
# summarization = 'NetSHy',
# BetweenShrinkage = 5)
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