EstimateQuality: Estimate the quality of imputation

In inzilico/imputeqc: A Quality Control for Genotype Imputation

Description

Counts the discordance of genotypes imputed.

Usage

EstimateQuality(origin, masks, imputed, id = NULL)

Arguments

origin	path to original unmasked file
masks	path/to/masks.RDS, where masks.RDS keeps the masks created upstream with GenerateMaskSet and saved as *.RDS.
imputed	vector of paths to files imputed. In the case of fastPHASE, the elements are path/to/*_genotypes.out. In the case of vcf files, the elements are path/to/*.vcf or path/to/*.vcf.gz. The order of elements of vector and masks should coincide.
id	character or numeric, id of computational experiment. If you run several calculations with different model parameter to find the optimal one, you can mark each run with id for the convinience of further visualization. The argument is optional.

Value

A data frame with two columns: "discordance" and "id". If id argument is not provided, only "discordance" is returned. It contains a proportion of wrognly imputed genotypes. By this we mean that one or two alleles are not coincided with the original ones. The function returns the values for one set of test files.

inzilico/imputeqc documentation built on July 28, 2020, 5:31 p.m.