dMatrix: Constructing D-Matrices

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

Constructing D-Matrices

Description

Estimating epimutation rates from high-throughput DNA methylation data

Usage

dMatrix(nodelist, cytosine, posteriorMaxFilter)

Arguments

nodelist	list of samples, you can find sample file in "extdata" called "nodelist.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/dm/","nodelist.fn", package="AlphaBeta")
df<-read.csv(file)
df$filename<-sub("^",paste0(dirname(file),"/"),df$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")
dMatrix(file, "CG", 0.99)

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