bootstrapCancerGenomes: Bootstrap a Mutation Count Matrix

Description Usage Arguments Value Note Author(s) References Examples

View source: R/bootstrapCancerGenomes.R

Description

Rearrange a Mutation count Matrix using the multivariate normal distribution. The function returns a bootstrapped Mutation Count matrix whose dimensions are identical to the input matrix

Usage

1

Arguments

genomes

a numeric matrix of Mutation Counts. Rows correspond to Mutation Types, columns to different samples

Value

a numeric matrix of Mutation Counts. Rows correspond to Mutation Types, columns to different samples

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.