estimate_error: 'Estimate genotyping error'

Description Usage Arguments Value Examples

View source: R/estimate_error.R

Description

Estimate error from data and pedigree.

Usage

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estimate_error(geno, ped, self_cutoff, depth_cutoff, check_kid_err = FALSE)

kid_het_err(geno, depth_cutoff, ped, pinfo, verbose)

count_geno(subgeno)

check_error(subgeno, depth_cutoff)

Arguments

geno

input object.

ped

a data.frame of pedigree information, must include three columns: proid (progeny id), parent1 (the first parent id), parent2 (the 2nd parent id).

check_kid_err

whether to check kids error based on the parental families.

imiss_cutoff

cutoff for individual missing rate, default=0.8.

size_cutoff

Minimum family size required for imputation, default=40.

Value

Return error matrix. See https://github.com/yangjl/imputeR/blob/master/vignettes/imputeR-vignette.pdf for more details.

Examples

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library(data.table, lib="~/bin/Rlib/")
ped <- read.table("data/parentage_info.txt", header =TRUE)
ped[, 1:3] <- apply(ped[, 1:3], 2, as.character)
geno <- fread("largedata/lcache/teo_recoded.txt")
estimate_error(geno, ped, self_cutoff=30, depth_cutoff=10)

yangjl/imputeR documentation built on May 4, 2019, 2:28 p.m.