dMatrix {AlphaBeta} | R Documentation |
Estimating epimutation rates from high-throughput DNA methylation data
dMatrix(genTable, cytosine, posteriorMaxFilter)
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 |
generating divergence matrices file.
## 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)