dMatrix: Constructing D-Matrices

Description Usage Arguments Value Examples

View source: R/D-matrices.R

Description

Estimating epimutation rates from high-throughput DNA methylation data

Usage

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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

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# 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)

AlphaBeta documentation built on Nov. 8, 2020, 6:30 p.m.