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SwitchBox Classifier for WHO 1999 Tumor Grading

classifier_grade_who_1999.Rd

A pre-trained SwitchBox classifier using Top Scoring Pairs (TSPs) methodology to predict bladder tumor grades according to the WHO 1999 classification system. The classifier distinguishes between low-grade (G1/G2) and high-grade (G3) tumors based on gene expression patterns.

Usage

classifier_grade_who_1999

Format

A list with 5 components:

name

Character string; classifier identifier (e.g., "283TSPs")

TSPs

Character matrix with 2 columns ("gene1", "gene2") containing gene pair identifiers for each comparison rule. Gene identifiers are symbols (e.g., "TP53", "BRCA1")

score

Named numeric vector of rule weights/importance scores, one per gene pair. Higher values indicate more discriminative rules

tieVote

Factor indicating voting behavior for tied comparisons

labels

Character vector of length 2: class labels c("G1G2", "G3")

Details

This classifier was trained on bladder cancer gene expression data to predict WHO 1999 histological grades. It uses rank-based gene pair comparisons that are robust to technical batch effects and normalization differences.

Usage:

  • Scores < 0.5 indicate low-grade tumors (G1/G2)

  • Scores ≥ 0.5 indicate high-grade tumors (G3)

Gene identifiers: Gene symbols (HUGO nomenclature)

Number of rules: Varies (check nrow(classifier_grade_who_1999$TSPs))

See also

classifier_grade_who_2022 for WHO 2022 grading, int_predict_grade to apply the classifier