FilterParamMD: Parameters for filtering results from the segmentation and...

Description Usage Arguments Examples

View source: R/methods-FilterParamMD.R

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

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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

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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)

MinimumDistance documentation built on Nov. 8, 2020, 11:11 p.m.