do.nmf: Perform Non-negative Matrix Factorization

Description Usage Arguments Value Note Author(s) References Examples

View source: R/do.nmf.R

Description

Perform Non-negative Matrix Factorization

Usage

1
do.nmf(v, r, params, verbose = TRUE)

Arguments

v

numeric matrix of Mutation Type Counts

r

numeric, number of signatures to extract

params

object (list) including all paramaters for running the analysis

verbose

logic, TRUE for printing information abouut the progress of the analysis

Value

list including two elements.

w

extracted signatures

h

contribution of each signature in all the samples of the input mut count matrix

Note

Affiliation: Meeks Lab, Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611 USA Software: Original MATLAB framework was described here: Cell Rep. 2013 Jan 31;3(1):246-59

Author(s)

Damiano Fantini

References

More info at: http://www.biotechworld.it/bioinf/2017/01/22/mutsignatures/

Examples

1
2
tmp <- getTestRunArgs(3)
do.nmf(v = tmp$v, r = tmp$r, params = tmp$params)

Example output

Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Loading required package: ggplot2

Attaching package: 'mutSignatures'

The following object is masked from 'package:utils':

    citation

.$w
            [,1]       [,2]
 [1,] 0.17547305 2.09888175
 [2,] 0.57972933 1.75876310
 [3,] 0.10983616 0.05352018
 [4,] 0.03582415 0.34841839
 [5,] 0.13631289 0.73869585
 [6,] 0.12303651 0.70401023
 [7,] 0.01003387 0.03702633
 [8,] 0.03274396 0.05282842
 [9,] 1.19751662 0.06117311

$h
         [,1]      [,2]      [,3]     [,4]
[1,] 72.33693  9.531291  8.687165 88.81569
[2,] 58.48901 65.111808 70.924978 53.95186

mutSignatures documentation built on May 30, 2017, 1:32 a.m.