maxlod: Maximum LOD score and Position

In atbroman/neqtl: Tools for analyzing expression QTL by position on genome

Description

Calculates maximum LOD score for each chromosome of a scanone object, and position of that max on the chromosome

Usage

maxlod(scan.out)

Arguments

scan.out

An object of class scanone. See scanone for details.

Value

Returns list of

maxlod	matrix of maximum LOD, made up of n rows and m columns, where n is the number of chromosomes in scanone object and m is the number of traits
maxlod.pos	List with n vectors of m positions, where n is the number of chromosmes in scanone and m is the number of traits

Note

Output from is mainly used in subsequent functions maxlod.sigpos,peaks, and findpeaks.traits

Author(s)

Karl W. Broman and Aimee Teo Broman

See Also

maxlod.sigpos peaks findpeaks.traits

Examples

data(fake.f2expr)
fake.f2expr <- calc.genoprob(fake.f2expr)

scan.f2 <- scanone(fake.f2expr,pheno.col=1:100, method="hk")
maxlod.f2 <- maxlod(scan.f2)

atbroman/neqtl documentation built on May 10, 2019, 2:08 p.m.