Relatedness-package: Maximum Likelihood Estimation of Relatedness using EM...

Description Details Author(s) Examples

Description

Inference of relatedness coefficients from a bi-allelic genotype matrix using a Maximum Likelihood estimation, Laporte, F., Charcosset, A. and Mary-Huard, T. (2017) <doi:10.1111/biom.12634>.

Details

This package infers the relatedness distribution coefficients for all couple of individuals in a set from their genotype, provided in a bi-allelic genotype matrix. The main function is 'RelCoef' which infers those coefficients. The arguments of this function are a genotype matrix for individuals and an frequency matrix that displays the allelic frequency at each marker in each population. Alternatively, a parental genotype matrix and a crossing matrix can be used. Additional information about structure membership can also be provided via a ParentPop vector (for more details see the help of 'RelCoef'). The main matrix is writen with C language, make sure you can use this code.

Author(s)

Fabien Laporte, Tristan Mary-Huard

Maintainer: Fabien Laporte <[email protected]>

Examples

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require('Relatedness')
data(Genotype)
data(Frequencies)
data(Cross)
RelCoef(IndividualGenom=matrix(0,ncol=0,nrow=0),ParentalLineGenom=Genotype,
Freq=Frequencies,Crossing=Cross,ParentPop=rep(1,20),Phased=TRUE,NbCores=2)

Example output

$Delta1
          [,1]       [,2]       [,3]       [,4]
[1,] 0.1872223 0.02379883 0.03671601 0.02792156
[2,] 0.0000000 0.14297271 0.01425833 0.04049574
[3,] 0.0000000 0.00000000 0.16347243 0.01492592
[4,] 0.0000000 0.00000000 0.00000000 0.17020904

$Delta2
     [,1]       [,2]         [,3]         [,4]
[1,]    0 0.01280921 0.0000463829 1.110553e-02
[2,]    0 0.00000000 0.0001783691 2.562746e-05
[3,]    0 0.00000000 0.0000000000 4.719932e-05
[4,]    0 0.00000000 0.0000000000 0.000000e+00

$Delta3
     [,1]       [,2]       [,3]         [,4]
[1,]    0 0.04242097 0.04553341 0.0191407481
[2,]    0 0.00000000 0.04916213 0.0006236025
[3,]    0 0.00000000 0.00000000 0.0190353346
[4,]    0 0.00000000 0.00000000 0.0000000000

$Delta4
     [,1]       [,2]       [,3]       [,4]
[1,]    0 0.02991431 0.04193678 0.05618873
[2,]    0 0.00000000 0.06626983 0.01860326
[3,]    0 0.00000000 0.00000000 0.06488061
[4,]    0 0.00000000 0.00000000 0.00000000

$Delta5
     [,1]       [,2]       [,3]       [,4]
[1,]    0 0.07745294 0.06158489 0.07175340
[2,]    0 0.00000000 0.01317127 0.08292124
[3,]    0 0.00000000 0.00000000 0.06403684
[4,]    0 0.00000000 0.00000000 0.00000000

$Delta6
     [,1]       [,2]       [,3]       [,4]
[1,]    0 0.03499694 0.03108816 0.03446088
[2,]    0 0.00000000 0.01037472 0.03636397
[3,]    0 0.00000000 0.00000000 0.03606032
[4,]    0 0.00000000 0.00000000 0.00000000

$Delta7
     [,1]       [,2]       [,3]       [,4]
[1,]    0 0.04034939 0.01504822 0.04564959
[2,]    0 0.00000000 0.04032412 0.04501147
[3,]    0 0.00000000 0.00000000 0.04619444
[4,]    0 0.00000000 0.00000000 0.00000000

$Delta8
     [,1]      [,2]       [,3]       [,4]
[1,]    0 0.0288133 0.08022405 0.05076399
[2,]    0 0.0000000 0.09865009 0.04982433
[3,]    0 0.0000000 0.00000000 0.07420835
[4,]    0 0.0000000 0.00000000 0.00000000

$Delta9
          [,1]         [,2]         [,3]         [,4]
[1,] 0.8127777 8.464521e-05 3.569369e-06 4.970672e-04
[2,] 0.0000000 8.570273e-01 4.161668e-05 6.143758e-05
[3,] 0.0000000 0.000000e+00 8.365276e-01 9.217594e-05
[4,] 0.0000000 0.000000e+00 0.000000e+00 8.297910e-01

$Delta10
     [,1]         [,2]         [,3]         [,4]
[1,]    0 0.0002435764 2.224204e-06 2.960255e-02
[2,]    0 0.0000000000 3.809295e-06 1.987441e-05
[3,]    0 0.0000000000 0.000000e+00 8.086918e-05
[4,]    0 0.0000000000 0.000000e+00 0.000000e+00

$Delta11
     [,1]      [,2]       [,3]       [,4]
[1,]    0 0.0538462 0.05138841 0.04976625
[2,]    0 0.0000000 0.06449816 0.08900609
[3,]    0 0.0000000 0.00000000 0.06854279
[4,]    0 0.0000000 0.00000000 0.00000000

$Delta12
     [,1]       [,2]       [,3]        [,4]
[1,]    0 0.08820768 0.05239152 0.008316945
[2,]    0 0.00000000 0.07913029 0.049942110
[3,]    0 0.00000000 0.00000000 0.037965919
[4,]    0 0.00000000 0.00000000 0.000000000

$Delta13
     [,1]       [,2]       [,3]        [,4]
[1,]    0 0.02101976 0.05805323 0.008704964
[2,]    0 0.00000000 0.05172596 0.069187525
[3,]    0 0.00000000 0.00000000 0.041759990
[4,]    0 0.00000000 0.00000000 0.000000000

$Delta14
     [,1]       [,2]       [,3]       [,4]
[1,]    0 0.06476529 0.06117117 0.03693132
[2,]    0 0.00000000 0.04672851 0.07392979
[3,]    0 0.00000000 0.00000000 0.03574802
[4,]    0 0.00000000 0.00000000 0.00000000

$Delta15
     [,1]     [,2]      [,3]      [,4]
[1,]    0 0.481277 0.4648120 0.5491965
[2,]    0 0.000000 0.4654828 0.4439839
[3,]    0 0.000000 0.0000000 0.4964212
[4,]    0 0.000000 0.0000000 0.0000000

Relatedness documentation built on Nov. 18, 2017, 4:12 a.m.