P-value graph

P-value graph to determine threshold for marker clustering

Usage

pValue(dist = seq(25,40, by = 5), pop.size = 100:500,
       map.function = "kosambi", LOD = FALSE)

Arguments

dist

Numeric range of genetic distances in cM.

pop.size

Numeric range of population sizes.

map.function

Character string of either "kosambi", "haldane", "morgan" or "cf" defining the mapping function to be used.

LOD

If LOD = TRUE the LOD score of linkage is calculated or if LOD = FALSE then the minus log10 p-value used to threshold the hoeffding inequality is calculated (defaults to FALSE).

Details

This function provides the ability to create a user specified p-value plot, as discussed in vignette("ASMap").

Value

A plot is displayed showing minus log10 pvalue (or LOD score) of linkage vs the range of specified population sizes for different specified genetic distances.

References

Taylor, J., Butler, D. (2017) R Package ASMap: Efficient Genetic Linkage Map Construction and Diagnosis. Journal of Statistical Software, 79(6), 1–29.

Author

Julian Taylor

See also

mstmap.cross and mstmap.data.frame

Examples

pValue(dist = seq(25, 40, by = 2))