buildPedigree: Building Pedigree

In jlab-code/AlphaBeta: Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants

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)

jlab-code/AlphaBeta documentation built on April 23, 2022, 11:02 a.m.