DSPRpeaks: Find and Summarize QTL

In egking/DSPRqtl: Analysis of DSPR phenotypes in R

Description

DSPRpeaks takes output from DSPRscan. Locates and summarizes QTL peaks.

Usage

DSPRpeaks(qtldat, method, threshold, LODdrop, BCIprob)

Arguments

qtldat	An object of class gscan. Output from DSPRscan.
method	a character string specifying the method to use for the confidence interval. Options are: 'LODdrop' calculates a LOD drop interval for the drop amount specified, 'BCI' calculates the Bayesian credible interval for the fraction specified, and 'both' calculates and returns both.
threshold	numeric vector of length one consisting of the signficance threshold. Default is 6.8 for inbred designs and 10.1 for the ABcross. Use DSPRperm to get a threshold specific to a given dataset.
LODdrop	numeric vector of length one consisting of the LOD drop to be used when using method 'LODdrop'. Default value is 2 which approximates a 95% confidence interval for the inbred designs. Users of the ABcross design should consider using a larger LOD drop.
BCIprob	numeric vector of length one consisting of the nominal Bayes fraction. Default value is 0.95.

Value

A list of class peaks containing a list for each significant peak, each containing:

threshold	the specified signficance threshold
peak	A single row data.frame with the chromosome, physical position (bp), genetic position (cM) and LOD score for the peak
LODdrop	the specified LOD drop for the support interval
CI	the upper and lower bounds of the confidence interval
founderNs	the number of RILs with each founder genotype at the peak
geno.means	the estimated means and standard errors for each founder genotype
perct.var	the percent variation explained by the QTL
entropy	the proporiton of missing information (entropy)

Author(s)

Elizabeth King ([e-mail])

egking/DSPRqtl documentation built on May 16, 2019, 12:14 a.m.