Function reference • xcore

All functions

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

%>%: re-export magrittr pipe operator

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