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imputeR

GBS data normally have high error rate for heterozygote sites. ImputeR is a package to infer the most likely genotypes using raw GBS data.

Install

Install devtools first, and then use devtools to install imputeR from github.

devtools::install_github("hadley/devtools")
library(devtools)
install_github("yangjl/imputeR")
library(imputeR)

Documentation

A vignette can be found here. Documented functions are listed as below. Their usage information can be found by typing ?function_name or help(function_name).

  • impute_parent

Utils

  • getsfs: setup the neutral SFS
  • error_mx and gen_error_mat: get genotype error matrix for mom and kids.