Package: CoGAPS 3.33.0

Elana J. Fertig

CoGAPS: Coordinated Gene Activity in Pattern Sets

Coordinated Gene Activity in Pattern Sets (CoGAPS) implements a Bayesian MCMC matrix factorization algorithm, GAPS, and links it to gene set statistic methods to infer biological process activity. It can be used to perform sparse matrix factorization on any data, and when this data represents biomolecules, to do gene set analysis.

Authors:Jeanette Johnson, Ashley Tsang, Jacob Mitchell, Thomas Sherman, Wai-shing Lee, Conor Kelton, Ondrej Maxian, Jacob Carey, Genevieve Stein-O'Brien, Michael Considine, Maggie Wodicka, John Stansfield, Shawn Sivy, Carlo Colantuoni, Alexander Favorov, Mike Ochs, Elana Fertig

CoGAPS_3.33.0.tar.gz
CoGAPS_3.33.0.zip(r-4.7)CoGAPS_3.33.0.zip(r-4.6)CoGAPS_3.33.0.zip(r-4.5)
CoGAPS_3.33.0.tgz(r-4.6-x86_64)CoGAPS_3.33.0.tgz(r-4.6-arm64)CoGAPS_3.33.0.tgz(r-4.5-x86_64)CoGAPS_3.33.0.tgz(r-4.5-arm64)
CoGAPS_3.33.0.tar.gz(r-4.7-arm64)CoGAPS_3.33.0.tar.gz(r-4.7-x86_64)CoGAPS_3.33.0.tar.gz(r-4.6-arm64)CoGAPS_3.33.0.tar.gz(r-4.6-x86_64)
CoGAPS_3.33.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CoGAPS/json (API)

# Install 'CoGAPS' in R:

install.packages('CoGAPS', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

GIST.data_frame - GIST gene expression data from Ochs et al.
GIST.matrix - GIST gene expression data from Ochs et al.
GIST.result - CoGAPS result from running on GIST dataset
GIST.uncertainty - GIST gene expression uncertainty matrix from Ochs et al.
modsimdata - Toy example to run CoGAPS on.
modsimresult - Result of applying CoGAPS on the Toy example.

On BioConductor:CoGAPS-3.33.0(bioc 3.24)CoGAPS-3.32.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

geneexpression transcription genesetenrichment differentialexpression bayesian clustering timecourse rnaseq microarray multiplecomparison dimensionreduction immunooncology cpp

6.55 score 178 scripts 14 mentions 37 exports 85 dependencies

Last updated from:6af7041f62. Checks:1 ERROR, 11 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	254
linux-devel-arm64	NOTE	385
linux-devel-x86_64	NOTE	446
source / vignettes	OK	465
linux-release-arm64	NOTE	381
linux-release-x86_64	NOTE	463
macos-release-arm64	NOTE	384
macos-release-x86_64	NOTE	666
macos-oldrel-arm64	NOTE	322
macos-oldrel-x86_64	NOTE	512
windows-devel	NOTE	604
windows-release	NOTE	529
windows-oldrel	NOTE	553
wasm-release	OK	278

Exports:binaryA buildReport calcCoGAPSStat calcZ checkpointsEnabled CoGAPS CogapsParams compiledWithOpenMPSupport findConsensusMatrix fromCSV getAmplitudeMatrix getClusteredPatterns getCorrelationToMeanPattern getFeatureLoadings getMeanChiSq getOriginalParameters getParam getPatternGeneSet getPatternMatrix getRetinaSubset getSampleFactors getSubsets getUnmatchedPatterns getVersion GWCoGAPS MANOVA patternMarkers plotPatternGeneSet plotPatternMarkers plotResiduals reconstructGene scCoGAPS setAnnotationWeights setDistributedParams setFixedPatterns setParam toCSV

Dependencies:abind BH Biobase BiocGenerics biocmake BiocParallel bitops brio callr caTools cli cluster codetools cowplot cpp11 crayon data.table DelayedArray desc diffobj dir.expiry dplyr evaluate farver fastmatch fgsea filelock forcats formatR fs futile.logger futile.options generics GenomicRanges ggplot2 glue gplots gtable gtools IRanges isoband jsonlite KernSmooth labeling lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats otel pillar pkgbuild pkgconfig pkgload praise processx ps R6 RColorBrewer Rcpp rhdf5 rhdf5filters Rhdf5lib rlang rprojroot S4Arrays S4Vectors S7 scales Seqinfo SingleCellExperiment snow SparseArray SummarizedExperiment testthat tibble tidyselect utf8 vctrs viridisLite waldo withr XVector

CoGAPS - Coordinated Gene Association in Pattern Sets

Rendered fromCoGAPS.Rmdusingknitr::rmarkdown

Last update: 2025-03-12
Started: 2018-08-02

Help page	Topics
CoGAPS: Coordinated Gene Activity in Pattern Sets	CoGAPS-package
binary heatmap for standardized feature matrix	binaryA binaryA,CogapsResult-method
Information About Package Compilation	buildReport
calculate statistic on sets of measurements (genes) or samples	calcCoGAPSStat calcCoGAPSStat,CogapsResult-method
probability gene belongs in gene set	calcGeneGSStat calcGeneGSStat,CogapsResult-method
compute z-score matrix	calcZ calcZ,CogapsResult-method
Check if package was built with checkpoints enabled	checkpointsEnabled
CoGAPS Matrix Factorization Algorithm	CoGAPS
CogapsParams constructor	CogapsParams
CogapsParams	CogapsParams-class
CogapsResult	CogapsResult-class
Check if compiler supported OpenMP	compiledWithOpenMPSupport
compute gene probability	computeGeneGSProb computeGeneGSProb,CogapsResult-method
find the consensus pattern matrix across all subsets	findConsensusMatrix
read CoGAPS Result object from a directory with a set of csvs see toCSV	fromCSV fromCSV,character-method
return Amplitude matrix from CogapsResult object	getAmplitudeMatrix getAmplitudeMatrix,CogapsResult-method
return clustered patterns from set of all patterns across all subsets	getClusteredPatterns getClusteredPatterns,CogapsResult-method
return correlation between each pattern and the cluster mean	getCorrelationToMeanPattern getCorrelationToMeanPattern,CogapsResult-method
return featureLoadings matrix from CogapsResult object	getFeatureLoadings getFeatureLoadings,CogapsResult-method
return chi-sq of final matrices	getMeanChiSq getMeanChiSq,CogapsResult-method
return original parameters used to generate this result	getOriginalParameters getOriginalParameters,CogapsResult-method
get the value of a parameter	getParam getParam,CogapsParams-method
generate statistics associating patterns with gene sets	getPatternGeneSet getPatternGeneSet,CogapsResult,list,character-method
return pattern matrix from CogapsResult object	getPatternMatrix getPatternMatrix,CogapsResult-method
get specified number of retina subsets	getRetinaSubset
return sampleFactors matrix from CogapsResult object	getSampleFactors getSampleFactors,CogapsResult-method
return the names of the genes (samples) in each subset	getSubsets getSubsets,CogapsResult-method
return unmatched patterns from each subset	getUnmatchedPatterns getUnmatchedPatterns,CogapsResult-method
return version number used to generate this result	getVersion getVersion,CogapsResult-method
GIST gene expression data from Ochs et al. (2009)	GIST.data_frame
GIST gene expression data from Ochs et al. (2009)	GIST.matrix
CoGAPS result from running on GIST dataset	GIST.result
GIST gene expression uncertainty matrix from Ochs et al. (2009)	GIST.uncertainty
Genome Wide CoGAPS	GWCoGAPS
constructor for CogapsParams	initialize,CogapsParams-method
Constructor for CogapsResult	initialize,CogapsResult-method
MANOVA statistical test for patterns between sample groups	MANOVA MANOVA,matrix,CogapsResult-method
Toy example to run CoGAPS on.	modsimdata
Result of applying CoGAPS on the Toy example.	modsimresult
compute pattern markers statistic	patternMarkers patternMarkers,CogapsResult-method
generate a barchart of most significant hallmark sets for a pattern	plotPatternGeneSet plotPatternGeneSet,list,numeric,numeric-method
heatmap of original data clustered by pattern markers statistic	plotPatternMarkers
plot of residuals	plotResiduals plotResiduals,CogapsResult-method
reconstruct gene	reconstructGene reconstructGene,CogapsResult-method
Single Cell CoGAPS	scCoGAPS
set the annotation labels and weights for subsetting the data	setAnnotationWeights setAnnotationWeights,CogapsParams-method
set the value of parameters for distributed CoGAPS	setDistributedParams setDistributedParams,CogapsParams-method
set the fixed patterns for either the A or the P matrix	setFixedPatterns setFixedPatterns,CogapsParams-method
set the value of a parameter	setParam setParam,CogapsParams-method
save CoGAPS Result object as a set of csvs to directory see fromCSV	toCSV toCSV,CogapsResult,character-method

Package: CoGAPS 3.33.0

CoGAPS: Coordinated Gene Activity in Pattern Sets

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)