Chip-seq Signal Quantifier Pipeline

Documentation for package ‘CSSQ’ version 1.5.1

ansTransform	Perform quantification and normalization of count data
calculatePvalue	Calculates P-value for the regions
calculateTvalue	Calculates modified T-statistics values for the given label and comparison
DBAnalyze	Performs differential binding analysis
getBgSubVal	Perform quantification and normalization of count data
getComparisons	Identify possible combinations
getNewLabels	Labels the samples according to the combinations from 'getComparisons'
getRegionCounts	Quantify region level count data
kmeansNormalize	Perform k-means clustering, normalize anscombe data and calculate cluster variances for a sample.
loadCountData	Load count data from input file.
normalizeData	Normalize anscombe transformed data
plotDist	Plot data distribution histograms
preprocessData	Wrapper function to preprocess the data