calcMD: Calculating the Minimum Distance matrix

In JMF47/DnMD: Detection of de novo deletion in targeted sequencing trios

Description

This function will return a matrix of minimum distances where ecah column is a family, and each row is a bin.

Usage

calcMD(mCounts, metaData)

Arguments

mCounts	A matrix of normalized coverage output by normalizedCounts().
metaData	A table in the format of the output of metaData().

Value

A data.frame of minimum distances. Each column is a trio, while each row is an entry in bins

Examples

load(system.file("extdata", 'bins.RData', package = "MDTS"))
load(system.file("extdata", 'counts.RData', package = "MDTS"))
load(system.file("extdata", 'pD.RData', package = "MDTS"))
mCounts <- normalizeCounts(counts, bins)
md <- calcMD(mCounts, pD)

JMF47/DnMD documentation built on May 31, 2019, 10:44 p.m.