pp.init: Parameter initialization function

In ASMap: Linkage Map Construction using the MSTmap Algorithm

Parameter initialization function

Description

Parameter initialization function for pushCross and pullCross

Usage

pp.init(seg.thresh = 0.05, seg.ratio = NULL, miss.thresh = 0.1,
        max.rf = 0.25, min.lod = 3)

Arguments

seg.thresh	Numerical value between zero and one determining the p-value threshold for the test of marker segregation distortion.
seg.ratio	A character string of the form "AA:BB" or "AA:AB:BB" describing the ratio of the alleles.
miss.thresh	Numerical value between zero and one determining the proportion of missing values.
max.rf	The maximum recombination fraction to consider when attempting to cluster pushed markers back into linkage groups.
min.lod	The minimum LOD score to consider when attempting to cluster pushed markers back into linkage groups.

Details

This parameter initialization function is used by the function pullCross to pull markers from a linkage map and pushCross to push markers back into a linkage map. How the arguments seg.thresh, seg.ratio and miss.thresh are used depends on which function is called. See pushCross and pullCross for more details.

Value

Return user defined parameter values for each of the parameters.

Author(s)

Julian Taylor

References

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

See Also

pushCross; pullCross

Examples

data(mapDH, package = "ASMap")

## pull markers from a linkage map with a segregation distortion

pars <- pp.init(seg.thresh = 0.05)
mapDH.s <- pullCross(mapDH, type = "seg.distortion", pars = pars)
mapDH.s$seg.distortion$table

ASMap documentation built on May 29, 2024, 1:48 a.m.