Length Counts

cfdna lengths writes <prefix>.length_counts.tsv.zst. Load fragment length-count TSV outputs and return counts, fractions, or densities as arrays, matrices, vectors, or data frames.

This is loader API documentation, not command-line help. See cfdna lengths for command flags and output generation.

Quick Use

Python

import cfdnalab as cfl

lengths = cfl.read_lengths("sample.length_counts.tsv.zst")

bins = lengths.length_bins()
counts = lengths.counts_array(with_length_range=(100, 221))
fractions = lengths.data_frame(value="fraction")

R

library(cfdnalab)

lengths <- read_lengths("sample.length_counts.tsv.zst")

bins <- length_bins(lengths)
counts <- length_counts_matrix(lengths, with_length_range = c(100L, 221L))
fractions <- length_data_frame(lengths, value = "fraction")

Notes

• Use with_lengths, with_length_range, or direct length-bin indices to select bins.
• For fractions and densities, denominator controls whether totals use all bins or selected bins.

Function Index

Python

Symbol	Type	Summary
read_lengths	function	Read a cfDNAlab length-count TSV and return the matching loader class.
LengthCounts	class	Common API for global, windowed, and grouped length-count outputs.
GlobalLengthCounts	class	Length counts for global output.
WindowedLengthCounts	class	Length counts for fixed-size or BED-window output.
GroupedLengthCounts	class	Length counts for grouped BED output.

Full details: Python API.

R

Topic	Summary
read_lengths	Loads a <prefix>.length_counts.tsv.zst file created with the cfdna lengths CLI command.
length_bins	Return length-bin metadata.
length_bin_idx	Look up the length-bin index containing a fragment length.
length_counts_matrix	Return length-count values as a matrix.
length_counts_vector	Return global length-count values as a vector.
length_data_frame	Return length-count values as a data frame.
window_metadata	Return window metadata.
group_metadata	Return group metadata.
group_idx	Look up a group index.

Full details: R API.