Importing Data
In NanoMethViz: Visualise methlation data from Oxford Nanopore sequencing

knitr::opts_chunk$set(echo = TRUE)

# preload to avoid loading messages
library(NanoMethViz)

library(NanoMethViz)

In order to use this package, your data must be converted from the output of methylation calling software to a special tabix format. Due to the use of the Unix sort function, this can only currently be done on a Linux or MacOS system.

We currently support output from

Nanopolish
f5c

The conversion can be done using the create_tabix_file() function. We provide example data of nanopolish output within the package, we can look inside to see how the data looks coming out of nanopolish

methy_calls <- system.file(package = "NanoMethViz",
    c("sample1_nanopolish.tsv.gz", "sample2_nanopolish.tsv.gz"))

# have a look at the first 10 rows of methy_data
methy_calls_example <- read.table(
    methy_calls[1], sep = "\t", header = TRUE, nrows = 6)

methy_calls_example

We then create a temporary path to store a converted file, this will be deleted once you exit your R session. Once create_tabix_file() is run, it will create a tabix file along with its index. Because we have a small amount of data, we can read in a small portion of it to see how it looks, do not do this with large datasets as it decompresses all the data and will take very long to run.

methy_tabix <- file.path(tempdir(), "methy_data.bgz")
samples <- c("sample1", "sample2")

# you should see messages when running this yourself
create_tabix_file(methy_calls, methy_tabix, samples)

# don't do this with actual data
# we have to use gzfile to tell R that we have a gzip compressed file
methy_data <- read.table(
    gzfile(methy_tabix), col.names = methy_col_names(), nrows = 6)

methy_data

Now methy_tabix will be the path to a tabix object that is ready for use with NanoMethViz. Please head over to the "Introduction" vignette to see how to use this data for visualisation!