genphys_fit: Model the relationship between genetical and physical genome...

In dmuijen/mapfuser: Construct Consensus Genetic Maps and Estimate Recombination Rates

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.

Author(s)

Dennis van Muijen

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)

## End(Not run)

dmuijen/mapfuser documentation built on May 28, 2019, 7:53 p.m.