MinimumDistance (version 1.16.0)

FilterParamMD: 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

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)