xcore expression regulators inference

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Documentation for package ‘xcore’ version 1.13.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

%>%	re-export magrittr pipe operator
addSignatures	Add molecular signatures to MultiAssayExperiment
applyOverColumnGroups	Apply function over groups of columns
applyOverDFList	Apply function over selected column in list of data frames
design2factor	Transform design matrix to factor
estimateStat	Estimate linear models goodness of fit statistic
filterSignatures	Filter signatures by coverage
fisherMethod	Combine p-values using Fisher method
getCoverage	Calculate regions coverage
getInteractionMatrix	Compute interaction matrix
getVarianceWeightedAvgCoeff	Calculate variance weighted average coefficients matrix
isTRUEorFALSE	Check if argument is a binary flag
mae	Calculate Mean Absolute Error
maeSummary	Helper summarizing MAE object
modelGeneExpression	Gene expression modeling pipeline
modelGeneExpression_ridge_regression_wraper	Ridge regression wrapper for modelGeneExpression
modelGeneExpression_significance_testing_wraper	Statistical testing of ridge regression estimates wrapper for modelGeneExpression
mse	Calculate Mean Squared Error
prepareCountsForRegression	Process count matrix for expression modeling
regressionData	Create MultiAssayExperiment object for expression modeling
remap_mini	xcore example molecular signatures
repVarianceWeightedAvgZscore	Calculate replicate variance weighted averaged Z-scores
ridgePvals	Significance testing in linear ridge regression
rinderpest_mini	xcore example expression data
rsq	Calculate $R^2$
simplifyInteractionMatrix	Simplify Interaction Matrix
stoufferZMethod	Combine Z-scores using Stouffer's method
subsetWithMissing	Subset keeping missing
translateCounts	Translate counts matrix rownames