calculateMindist: Deprecated function to calculate the minimum distance

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

Description

The 'minimum distance' is the minimum signed absolute difference of the parental log R ratios and the offspring log R ratios. Specifically, let |O-F| denote the absolute difference in the log R ratios comparing offspring to father and |O-M| the absolute difference in the log R ratios comparing offspring to mother. The minimum distance at a marker is the signed minimum of |O-M| and |O-F|. After segmentation of the minimum distance, non-zero segments can indicate a de novo difference in the log R ratio of the offspring and either parent. For example, a positive minimum distance suggests that the log R ratio from the offspring is greater than the log R ratio of either parent.

Usage

calculateMindist(object, ...)

## S4 method for signature 'TrioSet'
calculateMindist(object, verbose = TRUE, ...)

## S4 method for signature 'TrioSetList'
calculateMindist(object)

## S4 method for signature 'list'
calculateMindist(object, outdir = ldPath(), ...)

## S4 method for signature 'arrayORff_array'
calculateMindist(object, outdir, center, ...)

## S4 method for signature 'matrix'
calculateMindist(object, ...)

Arguments

object	see showMethods("calculateMindist")
...	Ignored
verbose	logical. Whether to display messages indicating progress.
outdir	character string indicating path to save output
center	ignored

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