dMatrix {AlphaBeta}R Documentation

Constructing D-Matrices

Description

Estimating epimutation rates from high-throughput DNA methylation data

Usage

dMatrix(genTable, cytosine, posteriorMaxFilter)

Arguments

genTable

Generation table name, you can find sample file in "extdata" called "generations.fn"

cytosine

Type of cytosine (CHH/CHG/CG)

posteriorMaxFilter

Filter value, based on posteriorMax ex: >= 0.95 or 0.99

Value

generating divergence matrices file.

Examples

## Get some toy data
file <- system.file("extdata","generations.fn", package="AlphaBeta")
df<-read.csv(file)
df$filename<-sub("^",paste0(dirname(file),"/"),df$filename )
write.csv(df, file = paste0(dirname(file),"/tm_generations.fn"),row.names=FALSE,quote=FALSE)
file <- system.file("extdata","tm_generations.fn", package="AlphaBeta")
dMatrix(file, "CG", 0.99)

[Package AlphaBeta version 1.0.0 Index]