findCI: Calculate LOD support interval
In egking/DSPRqtl: Analysis of DSPR phenotypes in R

Description Usage Arguments Value Author(s) References

findCI calculates the LOD support interval for a given LOD peak.

1	findCI(peakChr, peakPos, qtldat, method, LODdrop, BCIprob)

`peakChr`	character vector of length one. Must be one of the major chromosome arms in the Drosophila genome ('X','2L','2R','3L',or '3R').
`peakPos`	numeric vector of length one. A position in base pairs in the DSPR position list (every 10kb).
`qtldat`	`data.frame` of chromosome, position, and LOD scores (column names chr,Ppos,Gpos,LOD). List element LODscores 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.
`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.

A data.frame with two rows containing the chromosome, physical position (bp), genetic position (cM) and LOD scores corresponding to the lower and upper bound. A list of two data.frames are returned when the method used is 'both'.

Elizabeth King (kingeg@missouri.edu)

Manichaikul, A., J. Dupuis, S. Sen, and K.W. Broman. 2006. Performance of bootstrap confidence intervals for the location of a quantitative trait locus. Genetics 174: 481-489.

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