geno.impute: Impute GBS markers.

In trife/gbs: Tools for Genotyping-By-Sequencing Data

Description

Takes in a geno object and imputes markers using various methods.

Usage

geno.impute(geno, method, k = 4, maxiter = 10, n.core = 1, ...)

Arguments

geno	The geno object to impute. Each row is an individual and each column is a marker. Genotypic data is expected to be encoded as -1,0,1 for minor, het, and major, respectively.
method	The method to use for imputation. See details.
k	The number of clusters for KNN imputation.
maxiter	The maximum number of iterations for RF and SVD imputation.
n.core	The number of cores to use for RF imputation. This option is not available on Windows.
...	Additional arguments for rrBLUP::A.mat, randomForest::na.roughfix, and missForest::missForest

Value

A list with data frames corresponding to the methods used for imputation.

Methods

Markers can be imputed using mean, median, EM, Random Forest (RF), K Nearest Neighbors (KNN), and Singular Value Decomposition (SVD)

Author(s)

Chris Gaynor, [e-mail]

Trevor Rife, [e-mail]

Jessica Rutkoski, [e-mail]

Examples

data(wheat)
impute = geno.impute(hap$geno,c("mean","EM"))
impute$mean[1:10,1:20]
impute$EM[1:10,1:20]

trife/gbs documentation built on May 31, 2019, 7:53 p.m.