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Create a Compressed Methylation Call Archive (.ch3) from a calls file.

Source: R/make_mod_archive.R
make_mod_archive.Rd

Reads a delimited methylation call file and writes it to a compressed archive format. Useful for standardizing and compressing methylation data across multiple samples.

Usage

make_mod_archive(file_name, sample_name, out_path, short_ids = TRUE)

Arguments

file_name

Path to the input file (tab-delimited) containing methylation calls.

sample_name

Name of the sample to embed in the output archive filenames.

out_path

Output directory where the `.ch3` files will be written.

short_ids

Logical; default is `TRUE`, shortens `read_id` by trimming prefixes to reduce file size.

Value

(Invisibly) the path template to the output archive files. Also prints a message with timing information.

Details

The input file should contain specific columns such as `read_id`, `chrom`, `ref_position`, `ref_mod_strand`, `query_kmer`, `call_prob`, `call_code`, `base_qual`, and `flag`. The function filters out unplaced '-' strand reads with position 0, adds new fields like `start` and `end`, and writes the result as a compressed Arrow dataset with `zstd` compression.

Examples

if (FALSE) { # \dontrun{
make_mod_archive("calls.tsv", "sample1", "output/", short_ids = TRUE)
} # }