Output Loaders
The R and Python packages load files created by the cfdna command-line tool. They do not install, run, or wrap the CLI.
Use the CLI reference for command flags. Use these pages after you have output files and want to inspect, reshape, or plot them in R or Python.
Midpoint Profiles<prefix>.midpoint_profiles.zarr
Load midpoint profile Zarr stores and extract count arrays or data frames by group, fragment length bin, and midpoint position.
End-Motif Counts<prefix>.end_motifs.zarrLoad dense or sparse end-motif count Zarr stores and extract motif count tables, dense arrays, or sparse matrices.
Length Counts<prefix>.length_counts.tsv.zstLoad fragment length-count TSV outputs and return counts, fractions, or densities as arrays, matrices, vectors, or data frames.
Full API Indexes
- Python API: generated from public Python symbols and docstrings.
- R API: generated from roxygen
.Rdtopics for exported R functions and S3 generics.
Generation Sources
- Python documentation comes from
py-cfdnalab/src/cfdnalab. - R documentation comes from
r-cfdnalab/man, which is generated by roxygen fromr-cfdnalab/R.