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DESCRIPTION
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Package: pathwayPCA
Type: Package
Title: Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection
Version: 1.15.0
Authors@R: c(person("Gabriel", "Odom", email = "[email protected]", role = c("aut","cre")),
person("James", "Ban", email = "[email protected]", role = c("aut")),
person("Lizhong", "Liu", email = "[email protected]", role = c("aut")),
person("Lily", "Wang", email = "[email protected]", role = c("aut")),
person("Steven", "Chen", email = "[email protected]", role = c("aut")))
Description: pathwayPCA is an integrative analysis tool that implements the
principal component analysis (PCA) based pathway analysis approaches described
in Chen et al. (2008), Chen et al. (2010), and Chen (2011). pathwayPCA allows
users to: (1) Test pathway association with binary, continuous, or survival
phenotypes. (2) Extract relevant genes in the pathways using the SuperPCA and
AES-PCA approaches. (3) Compute principal components (PCs) based on the
selected genes. These estimated latent variables represent pathway activities
for individual subjects, which can then be used to perform integrative pathway
analysis, such as multi-omics analysis. (4) Extract relevant genes that drive
pathway significance as well as data corresponding to these relevant genes for
additional in-depth analysis. (5) Perform analyses with enhanced computational
efficiency with parallel computing and enhanced data safety with S4-class data
objects. (6) Analyze studies with complex experimental designs, with multiple
covariates, and with interaction effects, e.g., testing whether pathway
association with clinical phenotype is different between male and female
subjects.
Citations: Chen et al. (2008) <https://doi.org/10.1093/bioinformatics/btn458>;
Chen et al. (2010) <https://doi.org/10.1002/gepi.20532>; and
Chen (2011) <https://doi.org/10.2202/1544-6115.1697>.
License: GPL-3
Depends: R (>= 3.1)
Imports:
lars,
methods,
parallel,
stats,
survival,
utils
Suggests:
airway,
circlize,
grDevices,
knitr,
RCurl,
reshape2,
rmarkdown,
SummarizedExperiment,
survminer,
testthat,
tidyverse
biocViews:
CopyNumberVariation,
DNAMethylation,
GeneExpression,
SNP,
Transcription,
GenePrediction,
GeneSetEnrichment,
GeneSignaling,
GeneTarget,
GenomeWideAssociation,
GenomicVariation,
CellBiology,
Epigenetics,
FunctionalGenomics,
Genetics,
Lipidomics,
Metabolomics,
Proteomics,
SystemsBiology,
Transcriptomics,
Classification,
DimensionReduction,
FeatureExtraction,
PrincipalComponent,
Regression,
Survival,
MultipleComparison,
Pathways
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.2.3
Collate:
'CreatePathwayCollection.R'
'createClass_OmicsPath.R'
'createClass_validOmics.R'
'accessClass_OmicsPath.R'
'createClass_OmicsSurv.R'
'accessClass_OmicsSurv.R'
'accessClass_OmicsRegCateg.R'
'createClass_OmicsCateg.R'
'createClass_OmicsReg.R'
'accessClass_OmicsPathData.R'
'accessClass_pathwayCollection.R'
'accessClass_pathwayCollection_which.R'
'accessClass_pcOut.R'
'accessClass_pcOutpVals.R'
'aesPC_calculate_AESPCA.R'
'aesPC_calculate_LARS.R'
'aesPC_extract_OmicsPath_PCs.R'
'aesPC_permtest_CoxPH.R'
'aesPC_permtest_GLM.R'
'aesPC_permtest_LM.R'
'aesPC_unknown_matrixNorm.R'
'aesPC_wrapper.R'
'createOmics_All.R'
'createOmics_CheckAssay.R'
'createOmics_CheckPathwayCollection.R'
'createOmics_CheckSampleIDs.R'
'createOmics_JoinPhenoAssay.R'
'createOmics_TrimPathwayCollection.R'
'createOmics_Wrapper.R'
'data_colonSubset.R'
'data_genesetSubset.R'
'data_wikipathways.R'
'data_wikipathways_symbols.R'
'pathwayPCA.R'
'printClass_Omics_All.R'
'printClass_pathwayCollection.R'
'superPC_model_CoxPH.R'
'superPC_model_GLM.R'
'superPC_model_LS.R'
'superPC_model_tStats.R'
'superPC_model_train.R'
'superPC_modifiedSVD.R'
'superPC_optimWeibullParams.R'
'superPC_optimWeibull_pValues.R'
'superPC_pathway_tControl.R'
'superPC_pathway_tScores.R'
'superPC_pathway_tValues.R'
'superPC_permuteSamples.R'
'superPC_wrapper.R'
'utils_Contains.R'
'utils_adjust_and_sort_pValues.R'
'utils_load_test_data_onto_PCs.R'
'utils_multtest_pvalues.R'
'utils_read_gmt.R'
'utils_stdExpr_2_tidyAssay.R'
'utils_transpose_assay.R'
'utils_write_gmt.R'
VignetteBuilder: knitr
URL: <https://gabrielodom.github.io/pathwayPCA/>
BugReports: https://github.com/gabrielodom/pathwayPCA/issues