GOPCAConfig
class¶gopca.
GOPCAConfig
(user_params, gene_sets, gene_ontology=None, params=None)¶A GO-PCA configuration.
This class represents a complete set of inputs to the GO-PCA algorithm,
excluding the expression data. Specifically, the inputs consist of
parameter settings, represented by the GOPCAParams
class, as well as a
list of gene sets (optionally including Gene Ontology data; represented by
the genometools.ontology.GeneOntology
class).
Furthermore, two versions of the parameter settings are stored: The
first version (user_params
) holds the values exactly as specified by the
user. Some of those values can have special meaning, such as -1
for the
XL-mHG L
parameter (mHG_L
), which will be automatically converted
to p/8
(where p
is the number of genes). The second version
(simply called GOPCAParams class) holds the values actually used by the algorithm.
So in the previous example, the mHG_L
parameter stored in this version
would equal p/8
(rounded down to the nearest integer).
Parameters: |
|
---|
user_params
¶GOPCAParams
– The GO-PCA parameter settings, as specified by the user.
gene_sets
¶genometools.basic.GeneSetCollection
– The list of gene sets to be used by GO-PCA.
gene_ontology
¶genometools.ontology.GeneOntology
or None – The Gene Ontology (only if gene sets are based on GO annotations.)
params
¶GOPCAParams
or None – The final GO-PCA parameter settings, after resolving parameter values
with special meanings (see above).