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Input Format

Required Files

X Matrix (correlational PLS only)

CSV with subjects as rows and features as columns. The first column must be the subject identifier.

subject_id,region_A,region_B,region_C
sub01,1.23,4.56,7.89
sub02,2.34,5.67,8.90

Y Matrix

Same format as X. Subject IDs must match across files (order does not matter — the pipeline will align them).

Demographics

CSV with a subject ID column and at least one grouping column.

subject_id,group,sex,age
sub01,control,F,25
sub02,treatment,M,30

Optional Files

Feature Metadata

CSV with a feature column matching data column headers, plus category columns for plot colour-coding.

feature,category
region_A,frontal
region_B,frontal
region_C,temporal

Groups Configuration

YAML file for multiple grouping variables. See docs/usage.md for examples.

Subject Alignment

The pipeline finds the intersection of subject IDs across all input files. Subjects present in some files but not others are excluded with a warning. If no subjects are shared, the pipeline errors.

Missing Data

The pipeline does not handle missing data. If any value in X or Y is NaN, the pipeline errors and lists which subjects and features are affected.

See docs/missing-data.md for guidance on how to address this.