LRTools

Current package version: 0.1.0.0000 (beta)

Introduction

This is a small collection of the most useful functions I wrote during my master project. The package consists of functions that are necessary for the bioinformatics pipeline that I used to analyze Illumina HM450 and EPIC data. The package also includes other useful functions that can be helpful when analyzing DNA methylation data from these platforms.

Installation & Dependecies

To install this package use : devtools::install_github("LionelRohner/LRTools")
Following packages are required to use all functions of this package: matrixStats, pwr, ChAMP, ChAMPdata, akmedoids, ggplot2 If there are errors during the installation of ChAMP and ChAMPdata, try to install these packages first using :

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ChAMP")
BiocManager::install("ChAMPdata")

Functions

Beta_To_M

Conversion of beta-values to M-values.

champ.load_extended

Modified champ.load function from the \emph{ChAMP} package.

checkBMIQ

Plot the beta distribution of Infinium I and II probes before and after BMIQ-correction.

cohensD_Paired

Calculate Cohen's D effect size for paired data.

cohensD

Calculate standard Cohen's D effect size.

exVarPlot

Visualize explained variance of PC-1 and PC-2 of a matrix contaning only the most variable rows.

NamesDeltaBetaCut

Extraction of CpG-probes IDs or indices based on delta beta-values

powerCalc

Power and sample size estimation.

powerCalcPlot

Plotting PowerCalc Results.

topN_variableX

Find top most variable row entries in a microarray data matrix.