dMatrix: Constructing D-Matrices
In AlphaBeta: Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants
Description
Usage
Arguments
Value
Examples
Description
Estimating epimutation rates from high-throughput DNA methylation data
Usage
1
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
1
2
3
4
5
6
7
# 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.
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Description Usage Arguments Value Examples
Description
Estimating epimutation rates from high-throughput DNA methylation data
Usage
1 | 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
1 2 3 4 5 6 7 | # 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)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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