interpolate_cM: Interpolate genetic distances
View source: R/interpolate_cM.R
| interpolate_cM | R Documentation |
Interpolate genetic distances
Description
Creates monotone spline between physical (bp) and genetic (cM) distance
Usage
interpolate_cM(map, df = 8, max.extend = 5)
Arguments
map |
Data frame with four columns: marker, chrom, bp, cM |
df |
Degrees of freedom for the spline |
max.extend |
Maximum distance (in cM) to extrapolate beyond the end of the input map |
Details
The input map can be generated by merging an existing genetic map with positions in bp and cM with additional markers with only bp information. Interpolation is based on minimizing the mean-squared error between the original and interpolated positions in cM. For the df and max.extend parameters, use either a single integer (if same for all chromosomes) or a vector of length equal to the number of chromosomes.
Value
List containing
- map
Map data frame with additional column named cM.spline
- plot
ggplot2 object
