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Object Parameters

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mattjones315 edited this page Aug 18, 2017 · 2 revisions

Full List

  • data_file [FILE]

Input expression matrix file. This input is required and must go first. For formatting instructions see the Input file formats page

  • housekeeping [FILE]

Text file specifying houskeeping gene list to use when estimating dropout probabilities. One gene per line, identifiers should match row labels of data_file. This input must go second.

  • -signatures [FILE FILE FILE...]

Files containing gene signatures. Many files can be supplied here as a list. This input must go third.

  • precomputed [FILE [FILE ...]]

Files containing meta-data about the cells/samples. Labels (denoting information such as chemical stimuli) or numerical information (such as exposure time) are acceptable. For formatting instructions see the Input file formats page

  • scone (Optional)

Scone normalization data file.

  • norm_methods (Optional)

Normalization methods to be extracted from the scone object.

  • nofilter

If True, use all genes when creating projections. Default is False.

  • nomodel If True, no estimation of expression probability or false negative probability. Useful when input matrix is not single-cell data (population RNA-seq or lipidomics data, for example). Default is False.

  • filters

List of filters to compute for analysis. Default is a length 1 list of "fano".

  • debug

If 1, enable debugging features. Default is 0.

  • lean

If True, run a lean simulation where fewer projections are calculated. Default is False.

  • qc

If True, calculate QC. Default is False.

  • num_cores

Number of cores to utilized during analysis. Default is 1.

  • min_signature_genes

Minimum number of genes required to compute a score for a signature. Default is 5.

  • projections [FILE FILE ...]

List of file containing precomputed projections for analysis.

  • weights

Precomputed weights for each coordinate. Normally computed from the FNR curve.

  • threshold

Threshold to apply if threshold filter is applied.

  • perm_wPCA

If True, apply permutation wPCA to calculate significant number of PCs. Default is False.

  • sig_norm_method

Method to apply to normalize the expression matrix before calculating signature scores.

  • sig_score_method

Method to apply when calculating signature scores

  • exprData

Expression data matrix, which can be provided as opposed to a file path to an input expression matrix.

  • sigData

List of signatures, which can be provided as an alternative to file paths.

  • housekeepingData

Housekeeping data table, which can be provided as an alternative to a file path.

  • precomputedData

List of precomputed signature scores, as an alternative to a file path.

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