sspa_SVD

source

sspa_SVD(
   pathway_df, min_entity = 2, random_state = 0
)

---

Tomfohr et al 2005 PLAGE (SVD) method for single sample pathway analysis

Args

• pathway_df (pd.DataFrame) : pandas DataFrame of pathway identifiers (keys) and corresponding list of pathway entities (values).
• min_entity (int) : minimum number of metabolites mapping to pathways for ssPA to be performed Entity identifiers must match those in the matrix columns

Methods:

.fit

source

.fit(
   X, y = None
)

---

Fit the model with X.

Args

• X (pd.DataFrame) : pandas DataFrame omics data matrix consisting of m rows (samples) and n columns (entities). Do not include metadata columns

Returns

• self : object

.transform

source

.transform(
   X, y = None
)

---

Transform X.

Args

• X (pd.DataFrame) : pandas DataFrame omics data matrix consisting of m rows (samples) and n columns (entities). Do not include metadata columns

Returns

• self : object

.fit_transform

source

.fit_transform(
   X, y = None
)

---

Fit the model with X and transform X.

Args

• X (pd.DataFrame) : pandas DataFrame omics data matrix consisting of m rows (samples) and n columns (entities). Do not include metadata columns

Returns

• self : object

.fit_transform_

source

.fit_transform_(
   X, y = None
)

---

Fit the model with X and transform X.

Args

• X (pd.DataFrame) : pandas DataFrame omics data matrix consisting of m rows (samples) and n columns (entities). Do not include metadata columns

Returns

• self : object