End-Motif Counts

cfdna ends writes <prefix>.end_motifs.zarr. Load dense or sparse end-motif count Zarr stores and extract motif count tables, dense arrays, or sparse matrices.

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

Quick Use

Python

import cfdnalab as cfl

ends = cfl.read_end_motifs("sample.end_motifs.zarr")

storage = ends.storage_mode()
row_mode = ends.row_mode()
motifs = ends.motifs_metadata()

motif_counts = ends.data_frame(motifs="_AA")
motif_matrix = ends.sparse_counts_matrix(motifs="_AA")

R

library(cfdnalab)

ends <- read_end_motifs("sample.end_motifs.zarr")

storage <- storage_mode(ends)
row_mode <- row_mode(ends)
motif_table <- motifs(ends)

motif_counts <- end_motif_data_frame(ends, motifs = "_AA")
motif_matrix <- sparse_counts_matrix(ends, motifs = "_AA")

Notes

• Sparse stores stay sparse unless a dense helper explicitly receives a densify option.
• Windowed and grouped outputs can filter rows by max_blacklisted_fraction.

Function Index

Python

Symbol	Type	Summary
read_end_motifs	function	Open a cfDNAlab end-motif count Zarr store.
EndMotifCounts	class	Common API for global, windowed, and grouped end-motif outputs.
GlobalEndMotifCounts	class	End-motif counts for global output.
WindowedEndMotifCounts	class	End-motif counts for fixed-size or BED-window output.
GroupedEndMotifCounts	class	End-motif counts for grouped BED output.

Full details: Python API.

R

Topic	Summary
read_end_motifs	Loads a <prefix>.end_motifs.zarr store created with the cfdna ends CLI tool from the main cfDNAlab rust package.
storage_mode	Return the end-motif storage mode.
row_mode	Return the end-motif row mode.
motifs	For ordinary end-motif stores, the motif column contains concrete motif labels.
motif_idx	Look up a motif index.
has_motif	Test whether an end-motif label exists.
window_metadata	Return window metadata.
group_metadata	Return group metadata.
group_idx	Look up a group index.
end_motif_data_frame	Sparse outputs return stored non-zero rows unless the method explicitly receives densify = TRUE.
dense_counts_matrix	Sparse stores are not densified unless the method explicitly receives allow_densify = TRUE.
dense_counts_vector	Sparse stores are not densified unless the method explicitly receives allow_densify = TRUE.
sparse_counts_matrix	Sparse stores are converted directly from their stored COO arrays.
schema_version	Return the cfDNAlab schema version.

Full details: R API.