chessboard.api.io.Data

class chessboard.api.io.Data(reads, samples, lsvs, psi)

CHESSBOARD object for storing and manipulating data.

Stores splicing data and allows user to generate summary statistics and perform processing operations on the data.

Parameters

  • reads (ndarray) – A 2 x lsv x sample matrix containing junction spanning read outs. On the first axis, index 0 represents the number of junction spanning reads and index 1 represents the number of other reads in the normalization unit (e.g. LSV, intron cluster, entire gene, etc).

  • samples (ndarray) – Vector of sample names.

  • lsvs (ndarray) – Vector of LSV IDs.

  • psi (ndarray) – A lsv x sample matrix with PSI quantifications.

__init__(reads, samples, lsvs, psi)

Methods

__init__(reads, samples, lsvs, psi)

addChessboardOutput(filename)

Load results of CHESSBOARD algorithm into object.

subsetLSVs(index)

Retain only LSVs at the specified indicies.

subsetSamples(index)

Retain only samples at the specified indicies.

writeChessboardInput(filename)

Save data for input to CHESSBOARD algorithm.

writeGambitFile(filename)

Save data for input to GAMBIT visualization tool.

Attributes

num_lsvs

Number of LSVs

num_samples

Number of samples