doPatForCBN: Produces 'pat' files for H-CBN

In cbg-ethz/pathTiMEx: Joint Inference of Mutually Exclusive Driver Pathways and their Progression Dynamics

Description

doPatForCBN produces a binary matrix with dimensions patients x pathways, to be used as input by H-CBN. It can also write the matrix to a file.

Usage

doPatForCBN(groupsList, genesMat, write, path, name)

Arguments

groupsList	list with as many elements as mutually exclusive groups, each element consists of the genes assigned to the respective pathway
genesMat	binary alteration matrix with rows representing patients and columns representing genes, where an 1 indicates that a gene has been altered in one patient
write	boolean, indicating whether to also write the output matrix to a file. Default to FALSE.
path	path where the output matrix should be written. Default to "~/Dropbox/PathTiMEx/RPathTiMEx/txts".
name	name of the file to be written. Default to "outCBN".

Details

The matrix returned by this function is the binary alteration matrix on the basis of which order constraints between pathways are inferred. The input to this function are the assignment of genes to pathways (as a list) and the binary alteration matrix on the level of genes. A pathway is considered to be altered as soon as at least one of its gene members is altered. If write=TRUE and if path and name are provided, the matrix is written to the file path/name.pat.

Value

binary alteration matrix representing the alteration of pathways in patients.

Author(s)

Simona Constantinescu, [e-mail]

cbg-ethz/pathTiMEx documentation built on May 13, 2019, 2:03 p.m.