
                                                        

###~~~~ 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/>.
