estimateTransDist: 'transDist' parameter

In methimpute: Imputation-guided re-construction of complete methylomes from WGBS data

Description

Obtain an estimate for the transDist parameter (used in function callMethylation) by fitting an exponential function to the supplied correlations (from distanceCorrelation).

Usage

estimateTransDist(distcor, skip = 2, plot.parameters = TRUE)

Arguments

distcor	The output produced by distanceCorrelation.
skip	Skip the first n cytosines for the fitting. This can be necessary to avoid periodicity artifacts due to the context definition.
plot.parameters	Whether to plot fitted parameters on to the plot or not.

Value

A list() with fitted transDist parameters and the corresponding ggplot.

Examples

## Get some toy data
file <- system.file("data","arabidopsis_toydata.RData",
                    package="methimpute")
data <- get(load(file))
distcor <- distanceCorrelation(data)
fit <- estimateTransDist(distcor)
print(fit)

methimpute documentation built on Nov. 8, 2020, 5:47 p.m.