selectSNPs (version 1.0.1)

scoreLocal: Compute the weighted local score

Description

This function computes the weighted Local score, which is the weighted average between the U score and the E socre, with the weights given from the inputs.

Usage

scoreLocal(object, ...)
# S4 method for Chrom
scoreLocal(object, t1 = 1, t2 = 1, w1 = 0.5, w2 = 0.5)
# S4 method for Map
scoreLocal(object, chrom, t1 = 1, t2 = 1, w1 = 0.5, w2 = 0.5)

Arguments

object

A vector of minor allele frequency values.

...

Extra input parameters, as needed.

t1

A shrinkage parameter on the E score, which by default is 1.

t2

A shrinkage parameter on the U score, which by defaukt us 1.

w1

A weight for MAF, wchich by default is 0.5.

w2

A weight for map position, which by default is 0.5.

chrom

Names of chromosomes, for which local scores are to be computed; optioonal.

Value

The computed local score of the input object.

References

Wu XL, Li H, Ferretti R, Simpson B, Walker J, Parham J, Mastro L, Qiu J, Schultz T, Tait RG Jr, Bauck S, (2010). A unified local objective function for optimally selecting SNPs on arrays for agricultural genomics applications. Anim Genet. 2020 Jan 31. doi: 10.1111/age.12916.

Examples

# NOT RUN {
data("bov80K")
scoreLocal(bov80K)

# }