chessboard.api.io.createFromMajiq

chessboard.api.io.createFromMajiq(dir, outfilename, quant=10, miss=0.8)

Process and save MAJIQ generated data.

Extracts junction spanning read rates from MAJIQ [Vaquero-Garcia16] files and saves them in .npz format for downstream analysis. The .npz file is saved in outfilename.

Parameters

• dir (str) – Path to the .majiq files generated using the MAJIQ software.

• outfilename (str) – Path to the output .npz file.

• quant (int) – Minimum number of reads for junction to be quantifiable.

• miss (float) – Maximum fraction of samples for which a LSV is allowed to be missing before being removed.