gen.config: Generate configuration files for platypus

In graim/PLATYPUS: Multiple view and task learning

Description

Generate configuration files for platypus

Usage

gen.config(view.data, tasks, config.loc = "config",
  model.type = c("en", "rf", "svm"), view.filenames = NA,
  view.names = NA, ignore.label = "intermediate", store = FALSE)

Arguments

view.data	List of view data matrices. Must be named.
tasks	File containing all task labels, one column per task
config.loc	Where the config files should be stored
model.type	Type of classifier to use (select from en, rf, svm)
view.filenames	List of files containing view feature data
view.names	List of names for each view
ignore.label	Label to ignore in the task file (default 'intermediate')
store	Whether to store configs to file or not. Default FALSE.

Value

List of config filenames, for use in platypus

Examples

X1 <- matrix(rnorm(10000), nrow=100)
rownames(X1) <- paste0('Sample',seq(nrow(X1)))
colnames(X1) <- paste0('Feature',seq(ncol(X1)))
X2 <- matrix(rnorm(10000), nrow=100)
rownames(X2) <- paste0('Sample',seq(nrow(X2)))
colnames(X2) <- paste0('Feature',seq(ncol(X2)))
X3 <- matrix(rnorm(10000), nrow=100)
rownames(X3) <- paste0('Sample',seq(nrow(X3)))
colnames(X3) <- paste0('Feature',seq(ncol(X3)))
y <- sample(c('MOO','OINK',NA),100,replace=TRUE)
names(y) <- paste0('Sample',seq(max(nrow(X1), nrow(X2),nrow(X3))))

# Group together view and task data
view.data <- list(Farm=X1, Lion=X2, Cat=X3)
tasks <- as.data.frame(y)

# Pretend we loaded this data from some files
fn.view.names <- list(Farm='Farm.tsv', Lion='Lion.tsv', Cat='Cat.tsv')

# Generate config files
# If the data files don't already exist, use this
configs <- gen.config(view.data, tasks[,1,drop=FALSE], model.type='en', config.loc='config')

# Generate config files
gen.config(view.data[1], tasks[,1,drop=FALSE], model.type='en',config.loc='.')
gen.config(view.data, tasks, model.type='en', view.filenames=fn.view.names,config.loc='.')
gen.config(view.data, tasks, model.type='en',config.loc='.') 
gen.config(view.data, tasks, model.type='svm',config.loc='.')
gen.config(view.data, tasks, model.type='rf',config.loc='.')

graim/PLATYPUS documentation built on Oct. 4, 2019, 2:05 p.m.