estimateMapFromImputation: Re-estimate large gaps in a genetic map from IBD genotype...

Description Usage Arguments Details Value

View source: R/estimateMapFromImputation.R

Description

Re-estimate large gaps in a genetic map from IBD genotype imputations

Usage

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estimateMapFromImputation(
  mpcrossMapped,
  gapSize = 5,
  recombinationFractions = c(0:60/600, 11:49/100)
)

Arguments

mpcrossMapped

An object of class mpcrossMapped

gapSize

The size of the gap to reestimate.

recombinationFractions

The recombination fractions to use for numerical maximum likelihood estimation

Details

For larger gaps in a genetic map, the pairwise recombination fractions are not (by themselves) useful. An alternative is to estimate the IBD genotypes, and use the imputed IBD genotypes to re-estimate larger gaps using numerical maximum likelihood. Although the IBD genotypes are based on an existing genetic map, they may not be strongly affected by a large gap that has been poorly estimated, as the imputed IBD genotypes represent a consensus across all nearby markers, and also allow for genotyping errors. As a result, the re-estimated map may be different from the original map, and potentially more accurate.

Value

An object of class mpcrossMapped with a re-estimated map.


rohan-shah/mpMap2 documentation built on July 21, 2020, 8:58 p.m.