Perform Pathway Scoring
Summarizes the expression state of each pathway's genes into a single score.
 
Select method
 
1st PC - summarizes each pathway's expression state using the first principal component of its gene expression.
 
Pathifier - Uses the Pathifier algorithm (Drier et al., PNAS, 2013) to fit pathway data by mapping samples along a principal curve rather than a simple linear principal component.
 
Existing Scores - Rather than training pathway scores using the data, uses pre-defined gene weights to calculate a linear score summarizing pathway state.

 
Choose Baseline
Identifies the level of a categorical variable that defines a baseline subset of samples. These baseline samples provide orientation for pathway scores.
 
Adjust Pathway Score For
Fits pathway scores to the residuals of the selected variables. For example, adjusting for technical variables like binding density may be useful.
 
Plot Pathway Score Vs
Identifies variables to plot against the calculated pathway scores.