extract.r2.interval: Calculate the r^2 (squared correlation coefficient) between...

In gkeele/miqtl: Suite of QTL Mapping Functions

Calculate the r^2 (squared correlation coefficient) between the genotype at all loci on a chromosome and a specified SNP marker.

Description

This function primarily takes a formula, data frame, genome cache, and directory of founder strain .alleles files to calculate the pairwise r^2 between all individual markers and a specified locus, likely the peak SNP.

Usage

## S3 method for class 'r2.interval'
extract(scan.object, r2.scan.object, r2.level = 0.6)

Arguments

scan.object	An SNP scan object produced by imputed.snp.scan.h2lmm().
r2.scan.object	An r^2 object produced by pairwise.cor.snp.scan().
r2.level	DEFAULT: 0.6. The r^2 cutpoint. Returns the position interval includes loci with r^2 \ge r2.level.

Examples

extract.r2.interval()

gkeele/miqtl documentation built on Sept. 13, 2024, 5:49 a.m.