convertDMATRIX {AlphaBeta}R Documentation

convertDMATRIX

Description

calculate divergence times of the pedigree

Usage

convertDMATRIX(sample.info, branch.points, dmatrix, design)

Arguments

sample.info

input file containing information on generation times and pedigree lineages

branch.points

input file containing lineage branch points

dmatrix

input file containing 5mC divergence values for each sample pair

design

"sibling" or "direct"

Value

pedigree

Examples

## Get some toy data
file1 <- system.file("extdata/dm/","sampleInfo.csv", package="AlphaBeta")
file2<-system.file("extdata/dm/","branchPoints.csv", package="AlphaBeta")
file3<-system.file("extdata/dm/","AB-dMatrix-CG-0.99.csv", package="AlphaBeta")
sample.info <-read.table(file1,sep="\t", header=TRUE, stringsAsFactors = FALSE)
branch.points <-read.table(file2,sep="\t", header=TRUE, stringsAsFactors = FALSE)
dmatrix <-read.table(file3,sep="\t", header=TRUE, stringsAsFactors = FALSE)
pedigree <- convertDMATRIX(sample.info=sample.info,
 branch.points=branch.points,dmatrix=dmatrix,design="sibling")
head(pedigree)

[Package AlphaBeta version 1.0.0 Index]