Man pages for GabrielHoffman/pinnacle
pinnacle: Gene set enrichment analysis based on genomic intervals

correlationDecompCompute SVD of covariance matrix
correlationSquaredDecompCompute SVD of squared correlation matrix
dot-getScalingMatrixFromWeightsProjection on orthogal vector space
dot-get_SigmaGammaExtract scaling of random effects
dot-projectionOntoExistingSpaceProjection on orthogal vector space
dot-weight_fxn_internalScaled covariance between two peaks
ESSCompute effective sample size
evalCorrelationDecompEvaluate SVD of correlation structure
getCorrInGeneSetEvaluate correlation of genes within each gene set
getGeneMappingGet mapping from differential analysis to genomic annotations
getPeakGeneDistancesgetPeakGeneDistances
glsCovariance-classStore covariance for glslr
glsCovList-classStore list of covariances for glslr
glslrGeneralized least squares using precomputed eigen...
glslrApplyGeneralized least squares for many tests
glslr-classGeneralized least squares low rank
makeImageRectConvert correlation matrix into triangle plot
pinnacleEvaluate gene set enrichments with Pinnacle
pinnacleEnrichEvaluate enrichment statistics
plotCorrDistancePlot correlation versus distance
plotCorrTrianglePlot triangle of correlation matrix
plotDistanceWeightsPlot weights versus distance
plotEnrichmentPlot enrichment results
plotPinnacleResultPlot panels of results
print-glsCovariancePrint values
print-glsCovListPrint values
print-glslrPrint values
print-spectralDecompPrint values
projectionLMMProject response onto vector space
setDecompRankTruncate spectral decomposition
setDecompRank-methodsSet the rank of a spectralDecomp object by truncation
show-glsCovarianceShow values
show-glsCovListShow values
show-glslrShow values
show-spectralDecompShow values
spectralDecomp-classStore results of SVD and eigen decomposition in standard...
summary_glslr-classSummary of glslr
summary-glslr-methodSummarizing Generalized Linear Model Fits
vcov-methodsVariance-covariance matrix
weight_fxnScaled covariance between two peaks
GabrielHoffman/pinnacle documentation built on May 3, 2019, 3:02 p.m.