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 |
|
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.
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