GOPCA
class¶gopca.
GOPCA
(matrix, configs, **kwargs)¶Class for performing GO-PCA.
This class implements the GO-PCA algorithm. (The GO enrichment testing
is implemented in the enrichment.GeneSetEnrichmentAnalysis
class of
the genometools
package). The input data consists of an expression
matrix (genometools.expression.ExpMatrix
) and a list of GO-PCA
“configurations” (GOPCAConfig
), i.e., pairs of parameter settings and
gene set collections.
Parameters: |
|
---|
matrix
¶genometools.expression.ExpMatrix
– The expression matrix.
configs
¶list of GOPCAConfig
– The list of GO-PCA configurations. Each configuration consists of
gene sets (represented by a GOPCAGeneSets
instance) along with a set
of GO-PCA parameters (GOPCAParams
) to use for testing those gene
sets.
num_components
¶int –
pc_seed
¶int – The random number generator seed, used to generate the permutations for automatically determining the number of principal components to test.
pc_num_permutations
¶int – The number of permutations to used for automatically determining the number of principal components to test.
pc_zscore_thresh
¶float – The z-score threshold used for automatically determining the number of principal components (PC) to test. First, the fraction of variance explained by the first PC in each permuted dataset is calculated. Then, the mean and standard deviation of those values are used to calculate a z-score for the fraction of variance explained by each PC in the real dataset. All PCs with a z-score above the specified threshold are tested.
pc_max_components
¶int – The maximum number of principal components (PCs) to test (only relevant
when the algorithm for automatically determining the number of PCs
to test is used. For testing a fixed number of PCs, set the
num_components
attribute to a non-zero value.
verbose
¶bool – If set to True
, generate more verbose output.
estimate_num_components
()¶Estimate the number of non-trivial PCs using a permutation test.
print_signatures
(signatures, maxlength=50, debug=False)¶Print a list of signatures, sorted by PC and enrichment score.
run
()¶Perform GO-PCA.
Returns: | The GO-PCA run, or None if the run failed. |
---|---|
Return type: | GOPCARun or None |
set_param
(name, value)¶Set a GO-PCA parameter.
Parameters: |
|
---|---|
Returns: | |
Return type: |
simple_setup
(matrix, params, gene_sets, gene_ontology=None, **kwargs)¶Initialize GO-PCA instance with only one collection of gene sets.