Man pages for LTLA/csaw
ChIP-Seq Analysis with Windows

calculateCPMCalculate CPM
checkBimodalityCheck bimodality of regions
clusterFDRCompute the cluster-level FDR
clusterWindowsCluster DB windows into clusters
combineTestsCombine statistics across multiple tests
consolidateClustersConsolidate DB clusters
consolidateTestsConsolidate window statistics
consolidateWindowsConsolidate window sizes
correlateReadsCompute correlation coefficients between reads
csawUsersGuideView csaw user's guide
detailRangesAdd annotation to ranges
empiricalFDRControl the empirical FDR
extractReadsExtract reads from a BAM file
filterWindowsFiltering methods for RangedSummarizedExperiment objects
findMaximaFind local maxima
getBestTestGet the best test in a cluster
getPESizesCompute fragment lengths for paired-end tags
getWidthsGet region widths
maximizeCcfFind the delay at the maximal CCF
mergeWindowsMerge windows into clusters
mixedClustersTests for mixed DB clusters
normOffsetsNormalize counts across libraries
overlapStatsCompute overlap statistics
profileSitesProfile binding sites
readParamreadParam class and methods
regionCountsCount reads overlapping each region
scaledAverageScaled average abundance
SEmethodsSummarizedExperiment to DGEList
strandedCountsGet strand-specific counts
upweightSummitUpweight summits
windowCountsCount reads overlapping each window
wwhmWindow width at half maximum
LTLA/csaw documentation built on July 3, 2018, 12:46 a.m.