R: Clean up scantwo output

clean.scantwo {qtl} | R Documentation

## 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 not separated by `n.mar` markers, or that are less than `distance` cM apart, 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, n.mar=1, distance=0, ...)

### Arguments

`object` | An object of class `scantwo`. See `scantwo` for details.
`n.mar` | Pairs of positions not separated by at least this many markers have LOD scores set to 0.
`distance` | Pairs of positions not separated by at least this distance have LOD scores set to 0.
`...` | Ignored at this point.

### Value

The input scantwo object, with any negative or missing LOD scores replaced by 0, and LOD scores for pairs of positions separated by fewer than `n.mar` markers, or less than `distance` cM, are set to 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)
    out2cl2 <- clean(out2, n.mar=2, distance=5)

[Package qtl version 1.41-6 Index]