## ----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])