Mean and Variance information for full-sibs, half-sibs, first-cousins

Description

Computes theoretical mean and covariance matrix for k0 vs. k1 ibd coefficients for full-sib relationship along with inverse and eigenvalues/vectors of the covariance matrix.

Computes theoretical means and variances for half-sib relationship and for first-cousin relationship.

Usage

relationsMeanVar

Format

A list with the following entries:

FullSibs

list with following entries:

• mean: mean of (k0,k1) for full-sibs

• cov: covariance matrix for full-sibs

• invCov: inverse of the covariance matrix

• eigvals: eigenvalues of the inverse covariance matrix

• eigvectors: eigenvectors of the inverse covariance matrix

HalfSibs

list with following entries:

• mean: mean of (k0,k1) for half-sibs

• var: variance for half-sibs

FirstCousins

list with following entries:

• mean: mean of (k0,k1) for first-cousins

• var: variance for first-cousin

Source

computed by Cecelia Laurie using the referenced papers

References

Hill, W.G. and B.S. Weir (2011) Variation in actual relationship as a consequence of Mendelian sampling and linkage,Genet. Res., Camb., 93, 47–64.

Kong, X., et al (2004) A combined physical-linkage map of the human genome, American Journal of Human Genetics, 75, 1143–1148.

Examples

data(relationsMeanVar)
FS<-relationsMeanVar$FullSibs
FScov<-FS$cov   #gives covariance matrix for full-sibs
HS<-relationsMeanVar$HalfSibs
HSvar<-HS$var  #gives variance for half-sibs

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(GWASTools)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GWASTools/relationsMeanVar.Rd_%03d_medium.png", width=480, height=480)
> ### Name: relationsMeanVar
> ### Title: Mean and Variance information for full-sibs, half-sibs,
> ###   first-cousins
> ### Aliases: relationsMeanVar
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(relationsMeanVar)
> FS<-relationsMeanVar$FullSibs
> FScov<-FS$cov   #gives covariance matrix for full-sibs
> HS<-relationsMeanVar$HalfSibs
> HSvar<-HS$var  #gives variance for half-sibs
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>