alexg9010

# Combine methylKit annotation outputs into a single comprehensive dataframe

library(methylKit)
library(genomation)

## Generating setup with test data  -------
# this follows https://bioconductor.org/packages/devel/bioc/vignettes/methylKit/inst/doc/methylKit.html#4_Annotating_differentially_methylated_bases_or_regions
data("methylKit")
myDiff <- methylDiff.obj
myDiff25p <- methylKit::getMethylDiff(myDiff, difference = 25)

alexg9010

library(methylKit)

test_overflow <- function(n_samples, chunk_size) {
  # simulate 10 samples
  res <- dataSim(replicates = 10,
                 sites = 1e3,
                 treatment = rep(1, 10)) |>
    makeMethylDB(dbdir = tempdir()) |> # convert to tabix
    suppressMessages() |> 
    getDBPath() |>

alexg9010

---
title: "How to debug Rcpp code in a package"
output: html_document
author: Alexander Gosdschan  
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```