Estimate recombination rate

Share:

Description

Obtain a smoothed estimate of the recombination rate along a chromosome, using the cM and Mbp position of markers.

Usage

1
est.recrate(genmap, phymap, pos, window = 5)

Arguments

genmap

Vector of cM positions of markers, or a list of such vectors.

phymap

Vector of Mbp positions of markers, or a list of such vectors; same length as genmap.

pos

Vector of positions at which the recombination rate should be estimated, or a list of such vectors. If missing, we use the physical marker positions plus a grid with 4 positions per Mbp.

window

Length of sliding window (in Mbp).

Details

We assume constant recombination rate within each marker interval.

Value

A data.frame containing the positions and estimate recombination rates.

Author(s)

Karl W Broman, kbroman@biostat.wisc.edu

See Also

est.coi, intensity

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
# create equally-spaced map
pmap <- sim.map(100, n.mar=51, anchor=TRUE, include.x=FALSE, eq.spacing=TRUE)

# simulate cross
x <- sim.cross(pmap, type="bc", n.ind=501)

# estimate map for that cross
emap <- est.map(x)

# empirical estimate of recombination rate
rr <- est.recrate(emap[[1]], pmap[[1]], window=5)
plot(rr, type="l", lwd=2)