Description Usage Arguments Details Value See Also Examples
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.
1 2 3 4 |
object |
Object of class |
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 |
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
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.
The input mpcross object is returned with two additional components:
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. |
1 2 3 4 5 6 | 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)
|
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