corto {corto} R Documentation

## Calculate a regulon from a data matrix

### Description

This function applies Correlation and DPI to generate a robust regulon object based on the input data matrix and the selected centroids.

### Usage

corto(
inmat,
centroids,
nbootstraps = 100,
p = 1e-30,
verbose = FALSE,
cnvmat = NULL,
boot_threshold = 0
)


### Arguments

 inmat Input matrix, with features (e.g. genes) as rows and samples as columns centroids A character vector indicating which features (e.g. genes) to consider as centroids (a.k.a. Master Regulators) for DPI nbootstraps Number of bootstraps to be performed. Default is 100 p The p-value threshold for correlation significance (by default 1E-30) nthreads The number of threads to use for bootstrapping. Default is 1 verbose Logical. Whether to print progress messages. Default is FALSE cnvmat An optional matrix with copy-number variation data. If specified, the program will calculate linear regression between the gene expression data in the input matrix (exp) and the cnv data, and target profiles will be transformed to the residuals of each linear model exp~cnv. Default is NULL boot_threshold The fraction of bootstraps in which the edge should appear to be included in the final network. It can be any number between 0.0 and 1.0. Default is 0.0.

### Value

A list (object of class regulon), where each element is a centroid

• tfmode: a named vector containing correlation coefficients between features and the centroid

• likelihood: a numeric vector indicating the likelihood of interaction

### Examples

# Load data matrix inmat (from TCGA mesothelioma project)