Clean up scantwo output

Description

In an object output from scantwo, replaces negative and missing LOD scores with 0, and replaces LOD scores for pairs of positions that are between markers with 0. Further, if the LOD for full model is less than the LOD for the additive model, the additive LOD is pasted over the full LOD.

Usage

## S3 method for class 'scantwo':
clean(object)

Arguments

Value

The input scantwo object, with any negative or missing LOD scores replaced by 0, and LOD scores for positions between markers by 0. Also, if the LOD for the full model is less than the LOD for the additive model, the additive LOD is used in place of the full LOD.

Author(s)

Karl W Broman, kbroman@biostat.wisc.edu

See Also

scantwo, summary.scantwo

Examples

data(fake.f2)

fake.f2 <- calc.genoprob(fake.f2, step=5)
out2 <- scantwo(fake.f2, method="hk")
out2 <- clean(out2)