corto {corto} | R Documentation |

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

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

`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. |

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

# Load data matrix inmat (from TCGA mesothelioma project) load(system.file("extdata","inmat.rda",package="corto",mustWork=TRUE)) # Load centroids load(system.file("extdata","centroids.rda",package="corto",mustWork=TRUE)) # Run corto regulon <- corto(inmat,centroids=centroids,nthreads=2,nbootstraps=10,verbose=TRUE) # In a second example, a CNV matrix is provided. The analysis will be run only # for the features (rows) and samples (columns) present in both matrices load(system.file("extdata","cnvmat.rda",package="corto",mustWork=TRUE)) regulon <- corto(inmat,centroids=centroids,nthreads=2,nbootstraps=6,verbose=TRUE,cnvmat=cnvmat, p=1e-8)

[Package *corto* version 1.1.6 Index]