csaw: ChIP-Seq Analysis with Windows
Version 1.10.0

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

AuthorAaron Lun <alun@wehi.edu.au>, Gordon Smyth <smyth@wehi.edu.au>
Bioconductor views Annotation ChIPSeq Coverage DifferentialPeakCalling Genetics MultipleComparison Normalization Sequencing
Date of publicationNone
MaintainerAaron Lun <alun@wehi.edu.au>
LicenseGPL-3
Version1.10.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("csaw")

Popular man pages

detailRanges: Add annotation to ranges
empiricalFDR: Control the empirical FDR
extractReads: Extract reads from a BAM file
getPESizes: Compute fragment lengths for paired-end tags
profileSites: Profile binding sites
windowCounts: Count reads overlapping each window
wwhm: Window width at half maximum
See all...

All man pages Function index File listing

Man pages

checkBimodality: Check bimodality of regions
clusterFDR: Compute the cluster-level FDR
clusterWindows: Cluster DB windows into clusters
combineTests: Combine statistics across multiple tests
consolidateClusters: Consolidate DB clusters
consolidateSizes: Consolidate window sizes
correlateReads: Compute correlation coefficients between reads
csawUsersGuide: View csaw user's guide
detailRanges: Add annotation to ranges
empiricalFDR: Control the empirical FDR
extractReads: Extract reads from a BAM file
filterWindows: Filtering methods for RangedSummarizedExperiment objects
findMaxima: Find local maxima
getBestTest: Get the best test in a cluster
getPESizes: Compute fragment lengths for paired-end tags
getWidths: Get region widths
maximizeCcf: Find the delay at the maximal CCF
mergeWindows: Merge windows into clusters
mixedClusters: Tests for mixed DB clusters
normOffsets: Normalize counts between libraries
overlapStats: Compute overlap statistics
paramList: Get or modify readParam lists
profileSites: Profile binding sites
readParam: readParam class and methods
regionCounts: Count reads overlapping each region
scaledAverage: Scaled average abundance
SEmethods: Statistical wrappers for SummarizedExperiment objects
strandedCounts: Get strand-specific counts
upweightSummit: Upweight summits
windowCounts: Count reads overlapping each window
wwhm: Window width at half maximum

Functions

$,readParam-method Man page
activeChrs Source code
asDGEList Man page
asDGEList,SummarizedExperiment-method Man page
boundIntervals Source code
checkBimodality Man page Source code
checkLibSizes Source code
checkList Man page Source code
check_bimodality Source code
check_test_inputs Source code
clusterFDR Man page Source code
clusterWindows Man page Source code
coerceFragments Source code
collateExt Source code
combineOverlaps Man page Source code
combineTests Man page Source code
consolidateClusters Man page Source code
consolidateSizes Man page Source code
controlClusterFDR Man page Source code
correlateReads Man page Source code
correlate_reads Source code
csaw Man page
csawUsersGuide Man page Source code
decideStrand Source code
detailRanges Man page Source code
discardReads Source code
empiricalFDR Man page Source code
empiricalOverlaps Man page Source code
expandNA Source code
extendSE Source code
extendSEdir Source code
extractPE Source code
extractReads Man page Source code
extractSE Source code
filterWindows Man page Source code
findMaxima Man page Source code
formatColData Source code
getBestOverlaps Man page Source code
getBestTest Man page Source code
getGlobalBg Source code
getPESizes Man page Source code
getPValCol Source code
getWidths Man page Source code
getWindowNum Source code
make_one_sided Source code
maximizeCcf Man page Source code
mergeWindows Man page Source code
mixedClusters Man page Source code
mixedOverlaps Man page Source code
normOffsets Man page
normOffsets,SummarizedExperiment-method Man page
normOffsets,matrix-method Man page
normalize Man page
normalize,SummarizedExperiment-method Man page
overlapStats Source code
parseFCcol Source code
profileSites Man page Source code
profile_sites Source code
readParam Man page Source code
readParam-class Man page
reform Man page
reform,readParam-method Man page
reformList Man page Source code
regionCounts Man page Source code
region_counts Source code
runningWM Source code
scaledAverage Man page Source code
show,readParam-method Man page
strandedCounts Man page Source code
summitOverlaps Man page Source code
toGRanges Source code
upweightSummit Man page Source code
weightedFDR Source code
windowCounts Man page Source code
window_counts Source code
wwhm Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/asDGEList.R
R/basefun.R
R/checkBimodality.R
R/clusterFDR.R
R/clusterWindows.R
R/combineTests.R
R/consolidateSizes.R
R/correlateReads.R
R/csawUsersGuide.R
R/detailRanges.R
R/empiricalFDR.R
R/extractReads.R
R/filterWindows.R
R/findMaxima.R
R/getBestTest.R
R/getPESizes.R
R/maximizeCcf.R
R/mergeWindows.R
R/mixedClusters.R
R/normOffsets.R
R/overlapStats.R
R/paramList.R
R/profileSites.R
R/readParam.R
R/regionCounts.R
R/scaledAverage.R
R/strandedCounts.R
R/upweightSummit.R
R/windowCounts.R
build
build/vignette.rds
inst
inst/CITATION
inst/NEWS.Rd
inst/doc
inst/doc/csaw.Rnw
inst/doc/csaw.pdf
inst/doc/csawUserGuide.pdf
inst/doc/sra2bam.sh
inst/exdata
inst/exdata/autogen.R
inst/exdata/exrange.rds
inst/exdata/pet.bam
inst/exdata/pet.bam.bai
inst/exdata/pet.sam
inst/exdata/rep1.bam
inst/exdata/rep1.bam.bai
inst/exdata/rep2.bam
inst/exdata/rep2.bam.bai
inst/tests
inst/tests/run_all_tests.sh
inst/tests/simsam.R
inst/tests/test-best.R
inst/tests/test-best.Rout.save
inst/tests/test-bimodal.R
inst/tests/test-bimodal.Rout.save
inst/tests/test-ccf.R
inst/tests/test-ccf.Rout.save
inst/tests/test-chip.R
inst/tests/test-chip.Rout.save
inst/tests/test-cluster.R
inst/tests/test-cluster.Rout.save
inst/tests/test-combine.R
inst/tests/test-combine.Rout.save
inst/tests/test-cons.R
inst/tests/test-cons.Rout.save
inst/tests/test-detail.R
inst/tests/test-detail.Rout.save
inst/tests/test-empirical.R
inst/tests/test-empirical.Rout.save
inst/tests/test-empty.R
inst/tests/test-empty.Rout.save
inst/tests/test-filter.R
inst/tests/test-filter.Rout.save
inst/tests/test-maxima.R
inst/tests/test-maxima.Rout.save
inst/tests/test-merge.R
inst/tests/test-merge.Rout.save
inst/tests/test-overlap.R
inst/tests/test-overlap.Rout.save
inst/tests/test-pet3.R
inst/tests/test-pet3.Rout.save
inst/tests/test-profile.R
inst/tests/test-profile.Rout.save
inst/tests/test-region.R
inst/tests/test-region.Rout.save
man
man/SEmethods.Rd
man/checkBimodality.Rd
man/clusterFDR.Rd
man/clusterWindows.Rd
man/combineTests.Rd
man/consolidateClusters.Rd
man/consolidateSizes.Rd
man/correlateReads.Rd
man/csawUsersGuide.Rd
man/detailRanges.Rd
man/empiricalFDR.Rd
man/extractReads.Rd
man/filterWindows.Rd
man/findMaxima.Rd
man/getBestTest.Rd
man/getPESizes.Rd
man/getWidths.Rd
man/maximizeCcf.Rd
man/mergeWindows.Rd
man/mixedClusters.Rd
man/normOffsets.Rd
man/overlapStats.Rd
man/paramList.Rd
man/profileSites.Rd
man/readParam.Rd
man/regionCounts.Rd
man/scaledAverage.Rd
man/strandedCounts.Rd
man/upweightSummit.Rd
man/windowCounts.Rd
man/wwhm.Rd
src
src/Makevars
src/Makevars.win
src/annotator.cpp
src/bam_utils.cpp
src/bam_utils.h
src/best_in_cluster.cpp
src/check_bimodality.cpp
src/correlate_reads.cpp
src/csaw.h
src/find_maxima.cpp
src/get_cluster_stats.cpp
src/get_profile.cpp
src/get_rle_counts.cpp
src/init.cpp
src/merge_windows.cpp
src/pair_reads.cpp
src/single_reads.cpp
tests
tests/test-basic.R
tests/test-basic.Rout.save
vignettes
vignettes/csaw.Rnw
csaw documentation built on May 20, 2017, 10:46 p.m.

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