# xcore expression regulators inference

## Documentation for package ‘xcore’ version 1.16.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## 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