PathoFMPred: Tumour Feature Models from Pathology Representations

Builds and applies portable cancer-specific partial least squares (PLS) regression and partial least squares with linear discriminant analysis (PLS-LDA) model collections from pathology foundation-model representations. Feature and outcome tables are linked by explicit patient identifiers, repeated slide rows are pooled at patient level, and model development uses nested cross-validation before final fitting. The source package contains no fitted foundation-model parameters, embeddings, patient-level data, or atlas registry. Users may download a separately licensed, checksum-verified Prov-GigaPath collection after installation, or load authorized collections from local files. Outputs are research estimates without external-validation or clinical-use claims. The methods build on Wold et al. (2001) <doi:10.1016/S0169-7439(01)00155-1> and Barker and Rayens (2003) <doi:10.1002/cem.785>.

install.packages("PathoFMPred")

Try the PathoFMPred package in your browser