Package: CoGAPS 3.25.1

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

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CoGAPS.pdf |CoGAPS.html✨
CoGAPS/json (API)
NEWS

# 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-3.25.0(bioc 3.20)CoGAPS-3.24.0(bioc 3.19)

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

bioconductor-package

37 exports 2.38 score 81 dependencies 1 dependents 14 mentions

Last updated 23 days agofrom:5a8f4cc276

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 askpass BH Biobase BiocGenerics BiocParallel bitops caTools cli cluster codetools colorspace cowplot cpp11 crayon curl data.table DelayedArray dplyr fansi farver fastmatch fgsea forcats formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gplots gtable gtools httr IRanges isoband jsonlite KernSmooth labeling lambda.r lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats mgcv mime munsell nlme openssl pillar pkgconfig R6 RColorBrewer Rcpp rhdf5 rhdf5filters Rhdf5lib rlang S4Arrays S4Vectors scales SingleCellExperiment snow SparseArray SummarizedExperiment sys tibble tidyselect UCSC.utils utf8 vctrs viridisLite withr XVector zlibbioc

CoGAPS - Coordinated Gene Association in Pattern Sets

Jeanette Johnson, Ashley Tsang, Thomas Sherman, Genevieve Stein-O'Brien, Hyejune Limb, Elana Fertig

Rendered fromCoGAPS.Rmdusingknitr::rmarkdownon Jun 18 2024.

Last update: 2024-06-17
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 3.25.1

CoGAPS: Coordinated Gene Activity in Pattern Sets

CoGAPS - Coordinated Gene Association in Pattern Sets

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