props.R
In PROPS: PRObabilistic Pathway Score (PROPS)

## ---- include = FALSE---------------------------------------------------------
library(PROPS)

## ---- results=FALSE-----------------------------------------------------------
data(example_healthy)
example_healthy[1:5,1:5]

## ---- echo = FALSE, results = 'asis'------------------------------------------
knitr::kable(example_healthy[1:5,1:5])

## ---- results=FALSE-----------------------------------------------------------
data(example_data)
example_data[1:5,1:5]

## ---- echo = FALSE, results='asis'--------------------------------------------
knitr::kable(example_data[1:5,1:5])

## ---- results=FALSE-----------------------------------------------------------
props_features <- props(example_healthy, example_data)
props_features[1:5,1:5]

## ---- echo = FALSE, results='asis'--------------------------------------------
knitr::kable(props_features[1:5,1:5])

## ---- results = FALSE---------------------------------------------------------
healthy_batches = c(rep(1, 25), rep(2, 25))
dat_batches = c(rep(1, 20), rep(2, 30))

props_features_batchcorrected <- props(example_healthy, example_data, batch_correct = TRUE, healthy_batches = healthy_batches, dat_batches = dat_batches)
props_features_batchcorrected[1:5,1:5]

## ---- echo = FALSE, results='asis'--------------------------------------------
knitr::kable(props_features_batchcorrected[1:5,1:5])

## ---- results = FALSE---------------------------------------------------------
data(example_edges)
example_edges[1:8, ]

## ---- echo = FALSE, results='asis'--------------------------------------------
knitr::kable(example_edges[1:8, ])

## ---- results = FALSE---------------------------------------------------------
props_features_userpathways <- props(example_healthy, example_data, pathway_edges = example_edges)
props_features_userpathways[,1:5]

## ---- echo = FALSE, results='asis'--------------------------------------------
knitr::kable(props_features_userpathways[,1:5])