mpprob: Compute founder probabilities for multi-parent crosses

Description

Using haplotype probabilities, computes the probability that each location on a genome was inherited from each founder. Locations are run either at markers only, at the midpoints of all intervals or at step sizes of x cM. Probabilities can be computed using internally, or with R/happy.hbrem or R/qtl.

Usage

mpprob(object, chr, step = 0, mrkpos = TRUE, mapfx = c("haldane", "kosambi"), ibd = FALSE, threshold = 0.7, program = c("mpMap", "qtl", "happy"), tempfiledirectory = "", generations = 5)

Arguments

object

Object of class mpcross

chr

Subset of chromosomes

step

Step size (in cM) to create grid of positions at which to compute probabilities. At default value of 0, probabilities are calculated at marker positions only

threshold

Threshold for calling founder probabilities

mapfx

Map function used to convert map to recombination fractions

ibd

Flag to indicate whether to compute probabilities using IBD genotypes

mrkpos

Flag to indicate whether to compute probabilities at both marker positions and step size or just step size. Is overridden for step size of 0

program

R package to use to compute probabilities

tempfiledirectory

Directory in which to output temporary files. Default is current working directory

generations

Number of generations to assume in HAPPY. see happy

Value

prob: A list with founder probabilities for each chromosome. Format is a matrix with n.founders * n.markers columns and n.lines rows. Each group of n.founders columns will add up to 1. Founder probabilities are in the order of founders in the input founder matrix.
estfnd: A list with estimated founders for each chromosome. Format is a matrix with n.markers columns and n.lines rows. Missing values indicate where no founder probability exceeded the input threshold. Numeric values for founders indicate the row in the input founder matrix corresponding to the estimated founder.

Details

If program=="mpMap" then probabilities are computed using flanking markers at positions across the genome and represent 3-point haplotype probabilities. If program=="happy" then probabilities are computed using default values in R/happy.hbrem, which calculates ancestral haplotypes without using pedigree information. This only allows for probabilities to be computed at midpoints of intervals. If program=="qtl" then probabilities are computed from multipoint founder probabilities in R/qtl.

If step<0< code=""> for R/mpMap or R/qtl or step==0 for R/happy.hbrem, then probabilities are computed at the midpoints of marker intervals. However, if step==0 for R/qtl or R/mpMap, probabilities are computed only at marker locations.

Examples

Run this code

sim.map <- sim.map(len=rep(100, 2), n.mar=11, include.x=FALSE, eq.spacing=TRUE)
sim.ped <- sim.mpped(4, 1, 500, 6, 1)
sim.dat <- sim.mpcross(map=sim.map, pedigree=sim.ped, qtl=matrix(data=c(1, 50, .4, 0, 0, 0), nrow=1, ncol=6, byrow=TRUE), seed=1)
mpp.dat <- mpprob(sim.dat, program="qtl")
plot(mpp.dat)
summary(mpp.dat)