Provides genome-wide thresholds and tail probabilities for the maxima of genome scans using Poisson approximations.
tailprob(t,G,cross,type="1",d=0.01,cov.dim=0)
thresh(G,cross,type="1",p=c(0.10,0.05,0.01),d=0.01,cov.dim=0,
interval=c(1,40))
The function tailprob
returns the probability that the
genome-wide maximum LOD score exceeds a particular value. The
function thresh
returns genome-wide LOD thresholds
corresponding to a particular Type I error rate.
Genome size in centiMorgans.
LOD value for which tail probability is desired.
Vector giving the genome-wide Type I error for which thresholds are desired.
String indicating cross type which is "bc", for backcross, "f2" for intercross.
Type of LOD score for which threshold is desired. Right now the only option is "1", but more options will be added in the future.
Marker spacing in centiMorgans.
Dimension of interacting covariate. Set to 0 right now.
Interval over which to search for LOD threshold.
Saunak Sen, Jaya Satagopan, Karl Broman, and Gary Churchill
The tail probabilities are calculated using the method of
Dupuis and Siegmund (1999). The thresholds are calculated by solving
the tail probability equation using uniroot
. At this time only
one-dimensional thresholds are calculated, but this function will be
extended in the future.
Dupuis J and Siegmund D (1999) Statistical methods for mapping quantitative trait loci froma dense set of markers. Genetics 151:373-386.
tailprob(t=3,G=1440,cross="f2",d=10)
thresh(G=1440,cross="bc",d=10)
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