run: Run a pipeline

In jperezrogers/rabbit: An R Package to Create Computational Pipelines to Develop and Evaluate Biomarkers from High Dimensional Genomic Data

Description

A more detailed description will eventually go here...

Usage

run(pipeline, x, y, data = NULL, rank = NULL, outputdir = getwd(),
  iter = NULL, seed = NULL, force = FALSE, verbose = FALSE,
  exitOnError = FALSE, returnTraceback = TRUE)

Arguments

pipeline	an object of class Pipeline
x	a numerical matrix of gene expression values with samples in columns and genes in rows.
y	a two-level factor or numeric vector of length ncol(x) containing the outcome for each sample.
data	a data.frame with samples in rows and phenotype data in columns. nrow(data) must equal ncol(x).
rank	a numeric vector of length nrow(x) that can be passed to the sort function.
outputdir	directory where the results should be stored.
iter	an integer indicating the iteration to compute. See Details below.
seed	the numerical seed to set. Required when iter is not NULL. See Details below.
force	logical. Should existing results in outputdir be overwritten?
verbose	logical. Should intermediate text be printed to the screen?
exitOnError	should the pipeline run be aborted due to an error (TRUE) or should the pipeline simply skip the problematic model (FALSE)
returnTraceback	in the event of an error, should the error traceback be returned?

Details

More details to come...

Examples

## Not run: 
run(pipeline,x,y)

## End(Not run)

jperezrogers/rabbit documentation built on Feb. 9, 2020, 4:59 p.m.