est.recrate: Estimate recombination rate

In kbroman/xoi: Tools for Analyzing Crossover Interference

Estimate recombination rate

Description

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

Usage

est.recrate(genmap, phymap, pos = NULL, 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 NULL, 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, [e-mail]

See Also

est.coi(), intensity()

Examples

# 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)

kbroman/xoi documentation built on May 1, 2023, 9:35 p.m.