buildPedigree {AlphaBeta} | R Documentation

## Building Pedigree

### Description

calculate divergence times of the pedigree

### Usage

    buildPedigree(nodelist, edgelist, cytosine = "CG", posteriorMaxFilter = 0.99)

### Arguments

`nodelist` | input file containing information on generation times and pedigree lineages "extdata" called "nodelist.fn"
`edgelist` | input file containing edges
`cytosine` | Type of cytosine (CHH/CHG/CG)
`posteriorMaxFilter` | Filter value, based on posteriorMax

### Value

generating divergence matrices file.

### Examples

    # Get some toy data
    file <- system.file("extdata/dm/","nodelist.fn", package="AlphaBeta")
    df<-read.csv(file)
    df$filename <- gsub("^", paste0(dirname(dirname(file)),"/"), df$filename )
    write.csv(df, file = paste0(dirname(file),"/", "tmp_nodelist.fn"), row.names=FALSE, quote=FALSE)
    file <- system.file("extdata/dm/","tmp_nodelist.fn", package="AlphaBeta")
    file2 <- system.file("extdata/dm/","edgelist.fn", package="AlphaBeta")
    buildPedigree(nodelist = file, edgelist=file2, cytosine="CG", posteriorMaxFilter=0.99)

[Package AlphaBeta version 1.6.1 Index]