Description Usage Arguments Value Examples
View source: R/estimate_error.R
Estimate error from data and pedigree.
1 2 3 4 5 6 7 | 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)
|
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. |
Return error matrix. See https://github.com/yangjl/imputeR/blob/master/vignettes/imputeR-vignette.pdf for more details.
1 2 3 4 5 | 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)
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