FilterParamMD {MinimumDistance} | R Documentation

## Parameters for filtering results from the segmentation and copy number inference

### Description

A container for criteria used to filter the segmentation results post-hoc. Options including filtering on the posterior call, the posterior probability of the posterior call, the minimum number of markers spanned by the segment, the minimum width of the segment, and chromosome. Convenience functions are available for commonly used filters.

### Usage

    FilterParamMD(state = trioStateNames(), seqnames = paste0("chr", 1:22), ...)

### Arguments

`state` | trio copy number states to select
`seqnames` | chromosome names to select
`...` | additional arguments passed to `FilterParam-class`

### Examples

    library(VanillaICE)
    data(md_gr)
    data(md_exp)
    mdparam <- MinDistParam()
    fit <- MAP2(md_exp, md_gr, mdparam)
    ## return all segments
    segs(fit)

    ## Default filters
    param <- FilterParamMD()
    param
    cnvFilter(fit, param)

    param2 <- FilterParamMD(seqnames="chr22", probability=0.9, numberFeatures=10)
    cnvFilter(fit, param2)
    denovoHemizygous(fit)

[Package MinimumDistance version 1.38.0 Index]