README.md

In lb664/MethylCal: MethylCal: Bayesian Calibration of Methylation Levels

MethylCal

This package allows the calibration of methylation levels using MethylCal, a Bayesian calibration tool based on INLA (Rue et al., 2009). The package permits the visualisation of the calibration curve derived from standard controls with known methylation percentages for a selected assay. It also allows the correction of the methylation levels in case and control samples. If cases are provided, MethylCal performs a differential methylation test to detect hyper- and hypo-methylated samples. Besides MethylCal method, the package also includes the calibration and the correction provided by two alternative methods (Warnecke et al., 1997; Moskalev et al., 2011).

Installation

MethylCal has two dependencies, lattice and latticeExtra, that are automatically downloaded and installed. Another dependency R-INLA needs to be downloaded and installed manually. This is achieved by typing in the R command line

install.packages("INLA", repos = c(getOption("repos"), INLA = "https://inla.r-inla-download.org/R/stable"), dep = TRUE)

Once R-INLA has been installed (it may take a couple of minutes), installation of MethylCal requires the following steps:

1. Install the devtools package. This can be done from CRAN. Invoke R and then type

   install.packages("devtools")

2. Load the devtools package

   library(devtools)

3. Install MethylCal package by typing

   devtools::install_github("lb664/MethylCal", build_opts = c("--no-resave-data", "--no-manual"))

4. Finally, load the MethylCal package

   library(MethylCal)

Example

The example below allows to replicate Figure 3 C\&D in Ochoa et. (2019).

data(BWS_data)
AMP = c(0, 25, 50, 75, 100)
data = Formatting(BWS_data, AMP = AMP, n_Control = 15, n_Case = 18)
corr_data = MethylCalCorrection(data, Target = "KCNQ1OT1", n_Control = 15, n_Case = 18, printing = FALSE)

The output obtained by running MethylCalCorrection is transformed into a table with the same data format used in the uploaded data set with the function

output_data = TableFormatting(corr_data, n_Control = 15, n_Case = 18)

Further information

Further information can be found in the accompanying vignette by typing

vignette("MethylCal")

lb664/MethylCal documentation built on May 23, 2019, 4:02 a.m.