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

In rscharpf/MinimumDistance: A Package for De Novo CNV Detection in Case-Parent Trios

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)

rscharpf/MinimumDistance documentation built on Sept. 16, 2019, 4:12 a.m.