scoreLocal-methods: Compute the weighted local score

In selectSNPs: Optimal Selection of SNPs Using a Unified Local Function

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 signature 'Chrom'
scoreLocal(object, t1 = 1, t2 = 1, w1 = 0.5, w2 = 0.5)

## S4 method for signature '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.

Author(s)

Nick X-L Wu

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

data("bov80K")
scoreLocal(bov80K)

selectSNPs documentation built on Feb. 28, 2020, 5:08 p.m.