mackaay/WSHPackage

R package for the calculation of the following Within-Sample Heterogeneity Scores in Bisulfite Sequencing Data: FDRP, qFDRP, PDR, Epipolymorphism, Methylation Entropy and MHL

WSH

Short description

R package for the calculation of the following Intra-Sample Heterogeneity Scores in Bisulfite Sequencing Data: FDRP, qFDRP, PDR, Epipolymorphism, Methylation Entropy and MHL. The package is distributed under the GNU GPL-3 license, except for the external tools located in inst/bin (methclone, GNU Lesser GPL) and inst/scripts (MHL scripts, software distribution granted in the source file). All remaining code may be used, copied, changed and further distributed.

Installation

if(!requireNamespace("devtools")) install.packages("devtools",repos = "https://cloud.r-project.org/")
devtools::install_github("MPIIComputationalEpigenetics/WSHPackage")

Documentation

example.bam <- system.file(file.path("extData","small_example.bam"),
                           package="WSH")
example.rnb.set <- system.file(file.path("extData","small_rnbSet.zip"),
                               package="WSH")
example.rnb.set <- load.rnb.set(example.rnb.set)
set.option(coverage.threshold = 10)
qfdrp <- rnb.calculate.qfdrp(example.rnb.set,example.bam)

A more detailed documentation of the WSH R-package is available here.

Citation

If you are using this package, please cite:

• Scherer M., et al., Quantitative comparison of within-sample heterogeneity scores for DNA methylation data , Nucleic Acids Research, 2020, 10.1093/nar/gkaa120

Contact

You can contact Michael Scherer for reporting bugs, feature requests or questions.