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csaw (version 1.4.0)

ChIP-seq analysis with windows

Description

Detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control.

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Version

Version

1.4.0

License

GPL-3

Maintainer

Aaron Lun

Last Published

February 15th, 2017

Functions in csaw (1.4.0)

detailRanges

Add annotation to ranges
dumpPE

Dump paired-end data to file
upweightSummit

Upweight summits
windowCounts

Count reads overlapping each window
combineTests

Combine statistics across multiple tests
consolidateSizes

Consolidate window sizes
Parameter list methods

Get or modify readParam lists
overlapStats

Compute overlap statistics
wwhm

Window width at half maximum
makeExtVector

Make an extVector object
readParam

readParam class and methods
maximizeCcf

Find the delay at the maximal CCF
profileSites

Profile binding sites
extractReads

Extract reads from a BAM file
filterWindows

Filtering methods for RangedSummarizedExperiment objects
findMaxima

Find local maxima
clusterFDR

Compute the cluster-level FDR
mergeWindows

Merge windows into clusters
checkBimodality

Check bimodality of regions
SEmethods

Statistical wrappers for RangedSummarizedExperiment objects
normOffsets

Normalize counts between libraries
strandedCounts

Get strand-specific counts
getBestTest

Get the best test in a cluster
regionCounts

Count reads overlapping each region
scaledAverage

Scaled average abundance
csawUsersGuide

View csaw user's guide
correlateReads

Compute correlation coefficients between reads
getPESizes

Compute fragment lengths for paired-end tags
getWidths

Get region widths