following paper: Witten, Tibshirani and Hastie (2009) A
Packaged: Sun Apr 12 12:42:44 2009; dwitten

Author: Daniela Witten and Rob Tibshirani and Sam Gross

Package: PMA
Type: Package
Title: Penalized Multivariate Analysis
Version: 1.0.6
Date: 2009-12-04
Author: Daniela Witten and Rob Tibshirani and Sam Gross
Maintainer: Daniela Witten <dwitten@stanford.edu>
Description: Performs Penalized Multivariate Analysis: a penalized
matrix decomposition, sparse principal components analysis, and
sparse canonical correlation analysis, described in the
following papers: (1) Witten, Tibshirani and Hastie (2009) A
penalized matrix decomposition, with applications to sparse
principal components and canonical correlation analysis.
Biostatistics 10(3):515-534. (2) Witten and Tibshirani (2009)
Extensions of sparse canonical correlation analysis, with
applications to genomic data. Statistical Applications in
Genetics and Molecular Biology 8(1): Article 28.
License: GPL (>= 2)
Depends: R (>= 1.9.0), plyr
Packaged: Wed Apr 21 10:41:55 2010; dwitten
Repository: CRAN
Date/Publication: 2010-04-22 06:20:20

Packaged: Wed Feb 11 16:00:33 2009; dwitten

matrix decomposition, sparse principal components analysis,
and sparse canonical correlation analysis, described in
<doi:10.1093/biostatistics/kxp008> and Witten and Tibshirani
(2009) Extensions of sparse canonical correlation analysis,

Description: A modified version of PMA. The CCA() and CCA.permute() functions can also compute the
component-wise standard deviations of estimated U and V through
permutations in addition to standardize them. Furthermore, it computes
the non-parametric p-values for each components.
Performs Penalized Multivariate Analysis: a penalized matrix decomposition, sparse principal
components analysis, and sparse canonical correlation analysis, described in
Ali Mahzarnia, Alexander Badea (2022), "Joint Estimation of Vulnerable Brain Networks and Alzheimer’s Disease Risk Via Novel Extension of Sparse Canonical Correlation" at bioRxiv.

Title: Identify Prognosis-Related Pathways Altered by Somatic Mutation
person(given = "Yalan", family = "He", role  = "aut"),person(given = "Xiangmei", family = "Li", role  = "aut"))
Description: We innovatively defined a pathway mutation accumulate perturbation score (PMAPscore) to reflect the position and the cumulative effect of the genetic mutations at the pathway level. Based on the PMAPscore of pathways, identified prognosis-related pathways altered by somatic mutation and predict immunotherapy efficacy by constructing a multiple-pathway-based risk model (Tarca, Adi Laurentiu et al (2008) <doi:10.1093/bioinformatics/btn577>).
Imports: base, clusterProfiler, glmnet, graphics, grDevices, maftools,
org.Hs.eg.db, pROC, stats, survival, survminer, utils