Toolkit for the analysis of multi-state QTL data

Documentation for package ‘multistateQTL’ version 2.1.1

callSignificance	Call associations as significant in each state.
callSignificance-method	Call associations as significant in each state.
callSignificance<-	Call associations as significant in each state.
getComplete	Filter QTLExperiment based on missing data
getSignificant	Filter to only QTLs significant in at least one state
getTopHits	Filter QTLExperiment to keep only top hits
plotCompareStates	Compare QTL between two states
plotPairwiseSharing	Heatmap of pairwise QTL sharing with state-level annotations
plotQTLClusters	Heatmap of QTL across states
plotSimulationParams	Distribution of estimated simulation parameters
plotUpSet	Upset plot of QTL sharing between states with state-level annotations
qtleEstimate	Estimate parameters from real data for simulating multi-state QTL summary statistics
qtleParams	Default qtle simulation parameters
qtleParams2	Estimate parameters from real data for simulating multi-state QTL summary statistics
qtleSimulate	Create simulated multistateQTL data for testing purposes
replaceNAs	Return multistateQTL object with NAs filled in
runPairwiseSharing	Compute the proportion of (significant) QTL shared by pairs of conditions
runSignificantFeatures	Function to summarize QTL summary statistics by feature ID
runTestMetrics	Classify multi-state QTL
simPerformance	Performance metrics for multistateQTL simulations