mapfuser (version 0.1.2)

genphys_fit: Model the relationship between genetical and physical genome positions

Description

Fit a penalized thin plate regression spline (Wood, 2003) through genetic position in centiMorgan and physical genome positions in (Mega) base pairs.

Usage

genphys_fit(MF.obj, type = c("consensus", "map"), z = 5,
  chromosomes = NULL, map = NULL)

Arguments

MF.obj

A mapfuser object with a reference map loaded and either a consensus map created with mapfuser or a genetic loaded with read.maps

type

Fit physical genome positions vs. consensus genetic map made with mapfuser or an individual genetic map

z

discard invididual data points based on z-score threshold for scaled pearson residuals

chromosomes

The chromosomes to fit a P-spline, default to all chromosomes

map

Name of the genetic map to use when the consensus map is not used for fitting a P-spline and recombination rate calculation

Value

The input object is returned with added components recombination rate at a 0.1 Mbp interval, the general additive model fit (gam) with penalized spline fits per chromosome, and predictions of centiMorgan positions used for fitting. Markers that have been removed due to z-threshold are saved to the config slot.

Examples

# NOT RUN {
MF.obj <- genphys_fit(MF.obj, type = "consensus", z = 5, chromosomes = 1:5, map = NULL)
MF.obj <- genphys_fit(MF.obj, type = "map", z = 5, chromosomes = 1:5, map = "Col-0_Blh-1.csv")
# Plot the result
plot(MF.obj, which = "mareymap", maps = "consensus", chr = 1:5)
# }