Set Genetic Distance
Returns an updated bed.matrix with genetic
distances in centimorgan computed from the variant positions
set.dist(x, map, verbose = getOption("gaston.verbose", TRUE))x |
|
map |
The genetic map, given by a list of data frames (see Details) |
verbose |
If |
A map is a list of data frames, with names corresponding to chromosomes.
Each of these data frames must have columns pos and dist corresponding
to positions in bp and cM, respectively.
Such maps are too large to be included in a CRAN package. You can get two genetic
maps for the Human Genome (build 36 and 37) in the package HumanGeneticMap
on GitHub.
To install this package, run
install.packages("HumanGeneticMap", repos="https://genostats.github.io/R/")
You can then use this function with set.dist(x, HumanGeneticMap::genetic.map.b36)
for example, for positions on the build 36. Use map = HumanGeneticMap::genetic.map.b37)
for the build 37.
A bed.matrix similar to x, with updated values in x@snps$dist.
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