extract.chr.max.statistics.from.genomewide: Extracts chromosome-level statistics from the full output of...

In gkeele/miqtl: Suite of QTL Mapping Functions

Extracts chromosome-level statistics from the full output of genome-wide permutation scans, allowing chromosome-wide and genome-wide significance to be determined from the same output.

Description

This function extracts the associations for a specified chromosome from genome-wide permutation scans. This allows both genome-wide and chromosome-wide thresholds to be determined from the same output.

Usage

## S3 method for class 'chr.max.statistics.from.genomewide'
extract(full.perm.scans, chr, use.lod = FALSE)

Arguments

full.perm.scans	Output object from generate.qr.permutation.index.matrix().
chr	The chromosome that will have its association scores extracted from the full.perm.scans, essentially creating permutation scans specific to the chromosome.
use.lod	DEFAULT: FALSE. If TRUE, LOD scores are recorded. If FALSE, p-values are recorded, either based on the likelihood ratio test or ANOVA.

Examples

extract.chr.max.statistics.from.genomewide()

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