MCIBD: Monte Carlo Identity-By-Descent Matrix Estimation

This is a package implemented for flexible identity-by-descent (IBD) matrix estimation in F2 pedigrees. The IBD matrix estimate is approached by a Monte Carlo strategy, where the segregation of founder alleles is easy to define. Epistatic IBD matrices can also be calculated for two arbitrary loci. Such IBD matrix estimates are typically used in variance component quantitative trait loci (QTL) analysis. Parallelization is implemented to enhance the performance of Monte Carlo sampling.

Author
Xia Shen
Date of publication
None
Maintainer
Xia Shen <xia.shen@lcb.uu.se>
License
Unlimited
Version
0.4

View on R-Forge

Man pages

cnF2freq
Calculating Inheritance Probabilities using cnF2freq
MCIBD
Estimating Identity-By-Descent (IBD) Matrices using Monte...
MCIBD.chro
Estimating Identity-By-Descent (IBD) Matrices along A Whole...
MCIBD.epi2chro
Estimating Epistatic Identity-By-Descent (IBD) Matrices for...
MCIBD-package
Monte Carlo Identity-By-Descent Matrix Estimation
pedigree
A Pig Pedigree Information Dataset
probabilities
A Probailities Dataset of Pig Chromosome 6 from cnF2freq

Files in this package

MCIBD
MCIBD/NAMESPACE
MCIBD/data
MCIBD/data/datalist
MCIBD/data/pedigree.rda
MCIBD/data/probabilities.rda
MCIBD/R
MCIBD/R/MCIBD.R
MCIBD/R/MCIBD.epi2chro.R
MCIBD/R/cnF2freq.R
MCIBD/R/MCIBD.chro.R
MCIBD/inst
MCIBD/inst/other.zip
MCIBD/inst/MCIBD-manual.pdf
MCIBD/inst/other.tar
MCIBD/inst/doc
MCIBD/inst/doc/Sweave.sty
MCIBD/inst/doc/MCIBD.pdf
MCIBD/inst/doc/MCIBD_note_100819.pdf
MCIBD/inst/doc/pdfpages.dtx
MCIBD/inst/doc/MCIBD.Rnw
MCIBD/inst/doc/pdfpages.ins
MCIBD/DESCRIPTION
MCIBD/man
MCIBD/man/MCIBD.Rd
MCIBD/man/cnF2freq.Rd
MCIBD/man/MCIBD.chro.Rd
MCIBD/man/MCIBD-package.Rd
MCIBD/man/pedigree.Rd
MCIBD/man/MCIBD.epi2chro.Rd
MCIBD/man/probabilities.Rd