nullsims: Null distribution for Maximum LOD score

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

Description

Simulates a null distribution for the maximum LOD score for a genome scan of a single QTL model

Usage

nullsims(cross, n.sim = 1000, n.batch = 4, verbose = TRUE, ...)

Arguments

cross	An object of class cross. See read.cross for details.
n.sim	Number of simulations to run, default is 1000
n.batch	Number of batches, n.sim / n.batch should be around ~250
verbose	TRUE or FALSE, prints batch number
...	Additional parameters for scanone

Value

A numeric vector of maximum LOD scores, of length n.sim

Note

Use quantile(,probs=0.95) to determine LOD threshold for 5% false discovery rate

Recommend for n.sim>1000, code be run in BATCH mode

Author(s)

Karl W. Broman and Aimee Teo Broman

See Also

scanone quantile

Examples

data(hyper)
# Genotype probabilities
hyper <- calc.genoprob(hyper, step=2.5)

nd <- nullsims(hyper,n.sim=100,n.batch=1,method="hk")

quantile(nd,probs=0.95)

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