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Create a tabix file using methylation calls

Usage

create_tabix_file(
  input_files,
  output_file,
  samples = extract_file_names(input_files),
  verbose = TRUE
)

Arguments

input_files

the files to convert

output_file

the output file to write results to (must end in .bgz)

samples

the names of samples corresponding to each file

verbose

TRUE if progress messages are to be printed

Value

invisibly returns the output file path, creates a tabix file (.bgz) and its index (.bgz.tbi)

Examples

methy_calls <- system.file(package = "NanoMethViz",
    c("sample1_nanopolish.tsv.gz", "sample2_nanopolish.tsv.gz"))
temp_file <- paste0(tempfile(), ".tsv.bgz")

create_tabix_file(methy_calls, temp_file)
#> [2024-08-22 04:04:39] creating methylation table
#> processing /home/runner/work/_temp/Library/NanoMethViz/sample1_nanopolish.tsv.gz...
#> guessing file is produced by nanopolish...
#> processing /home/runner/work/_temp/Library/NanoMethViz/sample2_nanopolish.tsv.gz...
#> guessing file is produced by nanopolish...
#> [2024-08-22 04:04:40] sorting methylation table
#> [2024-08-22 04:04:40] compressing methylation table to tabix with index