qtlDesign (version 0.92)

Thresholds and tail probabilities: Calculating thresholds and tail probabilities for genome scans

Description

Provides genome-wide thresholds and tail probabilities for the maxima of genome scans using Poisson approximations.

Usage

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))

Arguments

G

Genome size in centiMorgans.

t

LOD value for which tail probability is desired.

p

Vector giving the genome-wide Type I error for which thresholds are desired.

cross

String indicating cross type which is "bc", for backcross, "f2" for intercross.

type

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.

d

Marker spacing in centiMorgans.

cov.dim

Dimension of interacting covariate. Set to 0 right now.

interval

Interval over which to search for LOD threshold.

Value

• 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.

Details

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.

References

Dupuis J and Siegmund D (1999) Statistical methods for mapping quantitative trait loci froma dense set of markers. Genetics 151:373-386.

See Also

uniroot.

Examples

tailprob(t=3,G=1440,cross="f2",d=10)
thresh(G=1440,cross="bc",d=10)