Quality Control Pipeline for ChIP-Seq Data


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Documentation for package ‘ChIC’ version 1.18.0

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chicWrapper ChIC analysis in one command
createMetageneProfile Wrapper function to create scaled and non-scaled metageneprofiles
downsample_ChIPpeaks Function for downsampling peaks in ChIP-data to simulate failed antibody
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
listMetrics Lists the metrics available 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