Midpoint Profiles

cfdna midpoints writes <prefix>.midpoint_profiles.zarr. Load midpoint profile Zarr stores and extract count arrays or data frames by group, fragment length bin, and midpoint position.

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

Quick Use

Python

import cfdnalab as cfl

profiles = cfl.read_midpoints("sample.midpoint_profiles.zarr")

groups = profiles.group_metadata()
length_bins = profiles.length_bins()
positions = profiles.positions()

profile = profiles.data_frame(groups="LYL1", with_lengths=167)

R

library(cfdnalab)

profiles <- read_midpoints("sample.midpoint_profiles.zarr")

groups <- group_metadata(profiles)
length_bins <- length_bins(profiles)
positions <- positions(profiles)

profile <- midpoint_data_frame(
  profiles,
  groups = "LYL1",
  with_lengths = 167
)

Notes

• Select groups or length bins before expanding to a data frame when the store is large.
• Python indices are zero-based. R indices are one-based.

Function Index

Python

Symbol	Type	Summary
read_midpoints	function	Open a cfDNAlab midpoint profile Zarr store.
MidpointProfiles	class	Helper for loading and slicing midpoint profile Zarr output.

Full details: Python API.

R

Topic	Summary
read_midpoints	Loads a <prefix>.midpoint_profiles.zarr store created with the cfdna midpoints CLI tool from the main cfDNAlab rust package.
group_metadata	Return group metadata.
length_bins	Return length-bin metadata.
positions	Return midpoint position-bin metadata.
group_idx	Look up a group index.
length_bin_idx	Look up the length-bin index containing a fragment length.
profile_array	Return one midpoint profile as an array vector.
midpoint_data_frame	Return midpoint profiles as a data frame.
midpoint_array	Return the full midpoint count array.
schema_version	Return the cfDNAlab schema version.

Full details: R API.