PCAPAM50
Enhanced 'PAM50' Subtyping of Breast Cancer
Accurate classification of breast cancer tumors based on gene expression data is not a trivial task, and it lacks standard practices.The 'PAM50' classifier, which uses 50 gene centroid correlation distances to classify tumors, faces challenges with balancing estrogen receptor (ER) status and gene centering. The 'PCAPAM50' package leverages principal component analysis and iterative 'PAM50' calls to create a gene expression-based ER-balanced subset for gene centering, avoiding the use of protein expression-based ER data resulting into an enhanced Breast Cancer subtyping.
README
###~~~~ 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/>.
Versions across snapshots
| Version | Repository | File | Size |
|---|---|---|---|
1.0.3 |
rolling linux/jammy R-4.5 | PCAPAM50_1.0.3.tar.gz |
1.1 MiB |
1.0.3 |
rolling linux/noble R-4.5 | PCAPAM50_1.0.3.tar.gz |
1.1 MiB |
1.0.3 |
rolling source/ R- | PCAPAM50_1.0.3.tar.gz |
1.1 MiB |
1.0.3 |
latest linux/jammy R-4.5 | PCAPAM50_1.0.3.tar.gz |
1.1 MiB |
1.0.3 |
latest linux/noble R-4.5 | PCAPAM50_1.0.3.tar.gz |
1.1 MiB |
1.0.3 |
latest source/ R- | PCAPAM50_1.0.3.tar.gz |
1.1 MiB |
1.0.3 |
2026-04-26 source/ R- | PCAPAM50_1.0.3.tar.gz |
1.1 MiB |
1.0.3 |
2026-04-23 source/ R- | PCAPAM50_1.0.3.tar.gz |
1.1 MiB |
1.0.3 |
2025-04-20 source/ R- | PCAPAM50_1.0.3.tar.gz |
1.1 MiB |