getrsq: Calculate imputation r squared

In BinaryDosage: Creates, Merges, and Reads Binary Dosage Files

Description

Routine to calculate the imputation r squared given the dosages and Pr(g=2). This is an estimate for the imputation r squared returned from minimac and impute2. The r squared values are calculated slightly differently between the programs. This estimate is based on the method used by minimac. It does well for minor allele frequencies above 5%. This function is used internally and is exported for use in examples.

Usage

getrsq(dosage, p0, p1, p2)

Arguments

dosage	Dosage values
p0	Pr(g=0) - unused
p1	Pr(g=1) - unused
p2	Pr(g=2)

Value

Imputation r squared

Examples

# Get information about binary dosage file
bdfile <- system.file("extdata", "vcf1a.bdose", package = "BinaryDosage")
bdinfo <- getbdinfo(bdfiles = bdfile)
snp1 <- getsnp(bdinfo = bdinfo, 1, dosageonly = FALSE)
rsq <- BinaryDosage:::getrsq(snp1$dosage, p2 = snp1$p2)

Example output

BinaryDosage documentation built on Jan. 13, 2020, 5:06 p.m.