GOPCASignature
class¶gopca.
GOPCASignature
(pc, gse_result, seed, matrix)¶A GO-PCA signature.
The goal of the GO-PCA algorithm is to define gene “signatures” that are likely to represent biologically relevant similarities and differences among samples.
A GO-PCA signature consists of a set genes and their expression profiles. Genes in a signature are related to each other in two ways:
Parameters: |
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pc
¶int – The principal component (PC) that the signature was derived from (starting at 1), with the sign of the integer indicating the way in which genes were ranked based on their PC loadings. If the sign is positive, then the signature was derived based on an ascending order. Conversely, if the sign is negative, then the signature was derived based on a descending ranking.
gse_result
¶RankBasedGSEResult
– The result of the XL-mHG test that was conducted after ranking the
genes based on their principal component loadings.
seed
¶genometools.expression.ExpProfile
– The seed used to determine gene membership during signature generation.
matrix
¶genometools.expression.ExpMatrix
– Gene-by-sample matrix containing the original expression values of
all signature genes.
Notes
Objects of this class are hashable, which allows them to be used in pandas Series and DataFrame indices.
K
¶The total number of genes annotated with the GO term.
X
¶The expression array.
escore
¶The E-escore of the enrichment test.
gene_set
¶The gene set that the signature is based on.
gene_set_id
¶The ID of the gene set that the signature is based on.
genes
¶The genes in the signature.
get_expression
(standardize=False, center=True, use_median=True)¶Generate an expression profile for the signature.
Parameters: |
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Returns: | The expression signature. |
Return type: |
get_figure
(sig_matrix=None, heatmap_kw=None, **kwargs)¶Generate a plotly figure showing the signature gene matrix as a heatmap.
This is a shortcut for Signature.get_heatmap(...).get_figure(...)
.
See ExpHeatmap.get_figure()
for keyword arguments.
Parameters: |
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Returns: | The plotly figure. |
Return type: |
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get_heatmap
(sig_matrix=None, standardize=False, center=True, use_median=True, include_id=False, include_stats=True, include_pval=True, cluster_genes=True, gene_cluster_metric=u'correlation', cluster_samples=True, sample_cluster_metric=u'euclidean', cluster_method=u'average', colorbar_label=None, **kwargs)¶Generate a heatmap of the signature gene matrix.
get_label
(max_name_length=0, include_stats=True, include_id=True, include_pval=False, include_coll=True)¶Generate a signature label.
k
¶The number of genes in the signature.
mHG_K
¶The total number of genes in the gene set.
mHG_N
¶The total number of genes in the analysis.
mHG_cutoff
¶The cutoff at which the XL-mHG test statistic was attained.
mHG_k
¶The number of genes within the gene set above the mHG cutoff.
n
¶The number of samples.
pval
¶The p-value of the enrichment test.
s
¶The signature expression vector.
samples
¶The sample labels.