imputeLDKNNi: LD KNNi imputation
In maize-genetics/rTASSEL: R Front-End for TASSEL

imputeLDKNNi

R Documentation

LD KNNi imputation

Description

This imputation algorithm uses LD to identify good predictors for each SNP, and then uses the high LD SNPs to identify K-Nearest Neighbors. The genotype is called with a weighted mode of the KNNs.

Usage

imputeLDKNNi(tasObj, highLDSSites = 30, knnTaxa = 10, maxDistance = 1e+07)

Arguments

`tasObj`	an rTASSEL `TasselGenotypePhenotype` object.
`highLDSSites`	Number of sites in high LD to use in imputation. Acceptable values are between `2` and `2000`. Defaults to `30`.
`knnTaxa`	Number of neighbors to use in imputation. Acceptable values are between `2` and `200`. Defaults to `10`.
`maxDistance`	Maximum physical distance between sites to search for LD (-1 for no distance cutoff - unlinked chromosomes will be tested). Defaults to `10e6`.