SNPgenmap: convert physical map positions on build 36 of the genome to genetic map positions

Description

Convert physical map positions on build 36 of the genome to genetic map positions by linear interpolation of the Rutgers combined linkage-physical map. The markers in the Rutgers map are a small subset of markers for which genetic map positions have been determined. Linear interpolation is done for points in between.

Usage

SNPgenmap(physmap, chromosomes)

Arguments

physmap

a vector of physical map positions on build 36 of the human genome

chromosomes

a vector containing the corresponding chromosome numbers

Value

The function returns a vector of genetic map positions.

Details

Genetic map positions are inferred from physical positions by linear interpolation of the Rutgers Combined Linkage-Physical Map for build 36 of the human genome, contained in the data object RutgersMapB36. Users who want some other form of interpolation can do so themselves using RutgersMapB36, as illustrated in the Examples. NB: The order of markers in RutgersMapB36 is the same for both physical and genetic maps. In order for an interpolated genetic map to preserve the ordering of physical map positions, the interpolant must be monotone increasing. Linear interpolation is monotone increasing, but other forms, such as spline interpolation, may not be.

Examples

Run this code

# NOT RUN {
data(Nhlsim)
gmap <- SNPgenmap(Nhlsim$physmap,Nhlsim$chromosome)

# Example of using RugtersMapB36 to do spline rather than linear 
# interpolation of genetic map positions on chromosome 1.  
# NB: Interpolant is not necessarily monotone increasing, which can lead to a 
# genetic map on which markers are re-ordered relative to the physical map.
data("RutgersMapB36")
chrmap<-splinefun(RutgersMapB36[["chr1"]]$Build36_map_physical_position,
                  RutgersMapB36[["chr1"]]$Sex.averaged_map_position)
c1ind<-(Nhlsim$chromosome=="chr1")
gmap[c1ind]<-chrmap(Nhlsim$physmap[c1ind])
# }