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###~~~~ PCAPAM50 PCAPAM50 is used to perform intrinsic subtyping for breast cancer gene expression data. PCAPAM50 leverages principal component analysis (PCA) and iterative PAM50 calls to derive the gene expression-based ER status. This generates an ER-balanced subset which is automatically used for gene centering and subsequent intrinsic calls. Thus, PCAPAM50 performs intrinsic subtyping in ER status unbalanced cohorts. #~ The package comes with a sample/TEST PAM50 matrix to demostrate runing the program. ####~~ 'TEST.ihc' and 'TEST.matrix' is provided ----subtitute these to make calls for your data ####~~ To make conventional intrinsic call that is only using IHC, use the function "makeCalls.ihc" ####~~ Refer to the Vignette to know more ###~~~~Prerequisites ##~~ Hardware Package should run on any computer (Linux/Unix, Windows or Mac) with R installed. However it is tested only on Linux/Ubuntu and Windows. ##~~Software #~~~ Required libraries lattice Biobase lattice ComplexHeatmap impute COPYRIGHT AND LICENSE --------------------- Copyright 2024 Windber Reseach Institute, Windber, PA - 15963. All Rights Reserved. Contact: Developer: Praveen K. Raj Kumar [P.RajKumar at wriwindber.org] Lab director: Xiaoying Lin[X.Lin at wriwindber.org] and Hai Hu [H.hu at wriwindber.org] This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.