Quality Control Pipeline for ChIP-Seq Data

Documentation for package ‘ChIC’ version 1.8.0

chicWrapper	Wrapper function to create a single document (pdf) that summarizes all plots produced by ChIC
createMetageneProfile	Wrapper function to create scaled and non-scaled metageneprofiles
getCrossCorrelationScores	QC-metrics from cross-correlation profile, phantom peak and general QC-metrics
getPeakCallingScores	Calculating QC-values from peak calling procedure
listAvailableElements	Shows available chromatin marks and factors
listDatasets	Lists the IDs of samples included in the compendium
metagenePlotsForComparison	Function to create metage plots for comparison
plotReferenceDistribution	Function to create reference distribution plot for comparison
predictionScore	Predict score
qualityScores_EM	Wrapper function to calculate EM metrics
qualityScores_GM	Wrapper function to calculate GM metrics from global read distribution
qualityScores_LM	Wrapper function that plots non-scaled profiles for TSS of TES and to collect the QC-metrics
qualityScores_LMgenebody	Wrapper function to plot the scaled metagene- profile and to collect the QC-metrics
readBamFile	Read bam file
removeLocalTagAnomalies	Removes loval anomalies
tagDensity	Smoothed tag density