MCIBD.epi2chro: Estimating Epistatic Identity-By-Descent (IBD) Matrices for...

In MCIBD: Monte Carlo Identity-By-Descent Matrix Estimation

Description

MCIBD.epi2chro estimates the epistatic IBD matrices for two given chromosomes. Monte Carlo sampling is used to approach to the matrix estimator, where the output file from cnF2freq is required. Segregation of the founder alleles can be set up in the estimation. Parallelzation is available using snowfall package if executing on a multi-core computer or cluster.

Usage

MCIBD.epi2chro(dis = 5, n.F2, pedigree = NULL, cnF2freq.out1 = NULL, 
               cnF2freq.out2 = NULL, IBD.type = "genotypic", 
			   output.Z = "none", read.file = FALSE, segregation = NULL, 
			   mc.size = 99, hpc = FALSE, n.cpus = 2)

Arguments

dis	the distance between two nearest test loci in centimorgan.
n.F2	an integer telling the number of F2 individuals in the pedigree.
pedigree	a matrix or data.frame or file containing pedigree information. For file (when read.file is TRUE), see pedi.ric in other.zip or other.tar for example.
cnF2freq.out1	a matrix or data.frame containing the output probabilities of chromosome 1 from cnF2freq. For file (when read.file is TRUE), see chro.ric in other.zip or other.tar for example.
cnF2freq.out2	a matrix or data.frame containing the output probabilities of chromosome 2 from cnF2freq. For file (when read.file is TRUE), see chro.ric in other.zip or other.tar for example.
IBD.type	a string specifying the output type of IBD matrix, "genotypic" or "gametic".
output.Z	a string indicates the type of output. If "av", average incidence matrix Z is estimated instead of the corresponding IBD matrix; If "all", the IBD matrix is still estimated as default but with all the incidence matrix imputes output in folder "Zall"; If "pc", an incidence matrix containing the principle components of the corresponding IBD matrix is output.
read.file	logical. If TRUE, data is loaded from files, where a pedigree information file is specified by pedigree and a probabilities output file cnF2freq.out in the working directory.
segregation	a vector specifying the segregation of founder alleles. (See Details.)
mc.size	an integer setting the sample size of the Monte Carlo sampling for one CPU.
hpc	logical. If TRUE, high performance computing is carried out by parallelization.
n.cpus	an integer telling the number of cores that parallelization is executed on. Only useful when hpc is TRUE. Not recommended when mc.size is small.

Details

To set up the segregation of the founder alleles, suppose that we have m founder(s) from one line and n from another line. Then in total there are 2 * (m + n) alleles needed to be set up. According to the order in the pedigree information file, these alleles for the founders should be filled in segregation as a vector with length 2 * (m + n). For instance, if there is one male in one line and three females in another line, the vector might be created like c(1,1,2,2,3,3,2,3), which means that the male has two identical alleles whereas the genotypes of the females are (2,2), (3,3) and (2,3), respectively. If NULL, all the founder alleles are assumed to be different from each other.

Value

Output IBD matrices are saved in the working directory as files named by the loci with extension .ibd.

Author(s)

Xia Shen

References

Shen, X., Nettelblad, C., Ronnegard, L. and Carlborg, O. (2009). Flexible Identity-By-Descent Matrix Estimation with Given Base Generation Structures in F2 Intercross Designs. Package Vignette.

See Also

MCIBD, MCIBD.chro, MCIBD-package

Examples

data(pedigree)
data(probabilities)

MCIBD.epi2chro(80, 191, pedigree, probabilities, probabilities, mc.size = 10)

MCIBD documentation built on May 2, 2019, 5:53 p.m.