Run the file-oriented NIPTmer sample workflow — niptmer_run

This is a thin convenience wrapper over the step-level utilities for the legacy niptmer segment: FASTQ -> .list -> count row -> combined table -> zscore -> XYA.

Usage

niptmer_run_sample(
  fastq_files,
  chr_list_dir,
  reference_table,
  control = NULL,
  out_dir,
  sample_name = NULL,
  k = 25,
  threads = 1,
  chromosomes = c(as.character(seq_len(22L)), "X", "Y"),
  chr_suffix = "_cleaned_25.list",
  keep_sample_list = FALSE,
  interpret_args = list(),
  ...
)

Arguments

fastq_files: One or more FASTQ file paths for the sample.
chr_list_dir: Directory containing chromosome list files.
reference_table: Reference count table as a data.frame or TSV path.
control: Passed to niptmer_score_samples().
out_dir: Output directory for generated artifacts.
sample_name: Sample identifier used for output files and appended row. By default it is inferred from the first FASTQ basename.
k: Word length passed to glistmaker.
threads: Number of threads passed to glistmaker.
chromosomes: Chromosomes to count in chr_list_dir.
chr_suffix: Chromosome list suffix inside chr_list_dir.
keep_sample_list: Whether to keep the generated sample .list file.
interpret_args: Named list of additional arguments passed to niptmer_write_xya().
...: Additional arguments passed to niptmer_write_zscore().

Value

A list with generated file paths and loaded data frames.