Quality Control Pipeline for ChIP-Seq Data


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Documentation for package ‘ChIC’ version 1.0.0

Help Pages

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
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 QC-metrics from cross-correlation analysis, QC-metrics designed for TFs and QC-metrics from peak-calls
qualityScores_GM Metrics taken 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