extractSignatures: Extract Signatures from Genomic Mutational Catalogs

Description Usage Arguments Value Note Author(s) References Examples

View source: R/extractSignatures.R

Description

Extract mutational signatures after the input Data and the input parameters have been checked and validated

Usage

1
extractSignatures(mutCountMatrix, params, verbose = TRUE)

Arguments

mutCountMatrix

numeric matrix of mutation counts

params

object (list) including all parameters for performing the analysis

verbose

logic, if TRUE the progress of the analysis will be printed to screen

Value

list including the following elements

Wall

extracted signatures

Hall

extracted effects

mutCounts.reconstructed

fitted values

mutCounts.errors

residuals

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()
extractSignatures(mutCountMatrix = tmp$mutCount.obj$mutCounts[1:10,1:3], 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

>.
$Wall
              [,1]         [,2]
 [1,] 2.788500e-01 3.300757e-01
 [2,] 2.944767e-01 3.793654e-01
 [3,] 3.200968e-01 2.163504e-01
 [4,] 2.683590e-02 2.610036e-02
 [5,] 6.511088e-03 2.134772e-02
 [6,] 1.280353e-02 2.120391e-03
 [7,] 2.361341e-02 1.441446e-02
 [8,] 2.589963e-02 3.574180e-17
 [9,] 4.931445e-17 3.889306e-03
[10,] 1.091292e-02 6.336324e-03

$Hall
             [,1]         [,2]     [,3]
[1,] 9.997428e-16 3.340000e+02 283.7694
[2,] 3.440000e+02 2.523661e-06 170.2306

$mutCounts.errors
$mutCounts.errors[[1]]
               [,1]          [,2]        [,3]
 [1,]  3.453966e+00  4.864107e+00 -8.31807295
 [2,]  4.982997e-01  6.447802e-01 -1.14307991
 [3,] -4.424522e+00 -1.091234e+01 15.33686403
 [4,]  2.147666e-02  3.680987e-02 -0.05828653
 [5,] -3.436144e-01 -1.747034e-01  0.51831778
 [6,]  2.705856e-01  2.723620e+00 -2.99420590
 [7,]  4.142441e-02  1.131213e-01 -0.15454573
 [8,] -1.209903e-14  3.495229e-01 -0.34952285
 [9,] -3.379211e-01 -9.815306e-09  0.33792113
[10,]  8.203044e-01  2.355085e+00 -3.17538907


$mutCounts.reconstructed
$mutCounts.reconstructed[[1]]
              [,1]         [,2]        [,3]
 [1,] 1.135460e+02 9.313589e+01 135.3180729
 [2,] 1.305017e+02 9.835522e+01 148.1430799
 [3,] 7.442452e+01 1.069123e+02 127.6631360
 [4,] 8.978523e+00 8.963190e+00  12.0582865
 [5,] 7.343614e+00 2.174703e+00   5.4816822
 [6,] 7.294144e-01 4.276380e+00   3.9942059
 [7,] 4.958576e+00 7.886879e+00   9.1545457
 [8,] 1.232107e-14 8.650477e+00   7.3495229
 [9,] 1.337921e+00 9.815306e-09   0.6620789
[10,] 2.179696e+00 3.644915e+00   4.1753891

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