Quality Control, Visualization and Processing for High-Throughput Sequencing data

Documentation for package ‘htSeqTools’ version 1.28.3

Help Pages

alignPeaks	Align peaks in a ChIP-Seq experiment by removing the strand specific bias.
alignPeaks-method	Align peaks in a ChIP-Seq experiment by removing the strand specific bias.
alignPeaks-methods	Align peaks in a ChIP-Seq experiment by removing the strand specific bias.
cmds	Classical Multi-Dimensional Scaling
cmds-method	Classical Multi-Dimensional Scaling
cmds-methods	Classical Multi-Dimensional Scaling
cmdsFit	Classical Multi-Dimensional Scaling for a distance matrix
cmdsFit-class	Class "cmdsFit"
cmdsFit-method	Classical Multi-Dimensional Scaling for a distance matrix
cmdsFit-methods	Classical Multi-Dimensional Scaling for a distance matrix
countHitsWindow	Compute number of hits in a moving window along the chromosome.
countHitsWindow-method	Compute number of hits in a moving window along the chromosome.
countHitsWindow-methods	Compute number of hits in a moving window along the chromosome.
coverageDiff	Compute the difference in coverage between two objects
enrichedChrRegions	Find chromosomal regions with a high concentration of hits.
enrichedChrRegions-method	Find chromosomal regions with a high concentration of hits.
enrichedChrRegions-methods	Find chromosomal regions with a high concentration of hits.
enrichedPeaks	Find peaks in sequencing experiments.
enrichedPeaks-method	Find peaks in sequencing experiments.
enrichedPeaks-methods	Find peaks in sequencing experiments.
enrichedRegions	Find significantly enriched regions in sequencing experiments.
enrichedRegions-method	Find significantly enriched regions in sequencing experiments.
enrichedRegions-methods	Find significantly enriched regions in sequencing experiments.
extendRanges	Extend reads or sequences by a user-specified number of bases.
extendRanges-method	Extend reads or sequences by a user-specified number of bases.
extendRanges-methods	Extend reads or sequences by a user-specified number of bases.
fdrEnrichedCounts	Posterior probability that a certain number of repeats are higher than expected by chance.
filterDuplReads	Detect and filter duplicated reads/sequences.
filterDuplReads-method	Detect and filter duplicated reads/sequences.
filterDuplReads-methods	Detect and filter duplicated reads/sequences.
findPeakHeight	FDR and optimal minHeight value estimation for ChIP-Seq peak calling with enrichedPeaks.
findPeakHeight-method	FDR and optimal minHeight value estimation for ChIP-Seq peak calling with enrichedPeaks.
findPeakHeight-methods	FDR and optimal minHeight value estimation for ChIP-Seq peak calling with enrichedPeaks.
getCover	Class "gridCover"
getCover-method	Class "gridCover"
getViewsInfo	Class "gridCover"
getViewsInfo-method	Class "gridCover"
giniCoverage	Compute Gini coefficient.
giniCoverage-method	Compute Gini coefficient.
giniCoverage-methods	Compute Gini coefficient.
gridCover-class	Class "gridCover"
gridCoverage	Compute coverage on user specified genomic regions.
htSample	Example ChIP-sequencing data with 2 replicates per group obtained in two different dates.
islandCounts	Find genomic regions with high coverage and count number of reads overlapping each region in each sample
islandCounts-method	Find genomic regions with high coverage and count number of reads overlapping each region in each sample
islandCounts-methods	Find genomic regions with high coverage and count number of reads overlapping each region in each sample
lines-method	Class "gridCover"
listOverlap	Assess the overlap between two or three lists.
listOverlap-method	Assess the overlap between two or three lists.
listOverlap-methods	Assess the overlap between two or three lists.
mergeRegions	Merge nearby chromosomal regions.
mergeRegions-method	Merge nearby chromosomal regions.
mergeRegions-methods	Merge nearby chromosomal regions.
PeakLocation	Peak density with respect to closest gene.
PeakLocation-method	Peak density with respect to closest gene.
PeakLocation-methods	Peak density with respect to closest gene.
plot-method	Class "gridCover"
plot-method	Methods for Function plot in Package 'htSeqTools'
plotChrRegions	Plot chromosomal regions of interest
plotMeanCoverage	Peak density with respect to closest gene.
plotMeanCoverage-method	Peak density with respect to closest gene.
plotMeanCoverage-methods	Peak density with respect to closest gene.
plotminHeight	FDR and optimal minHeight value estimation for ChIP-Seq peak calling with enrichedPeaks.
regionsCoverage	Compute coverage on user specified genomic regions.
regionsCoverage-method	Compute coverage on user specified genomic regions.
regionsCoverage-methods	Compute coverage on user specified genomic regions.
rowLogRegLRT	Row-wise logistic regression
show-method	Class "gridCover"
ssdCoverage	Standardized SD of the genomic coverage
ssdCoverage-method	Standardized SD of the genomic coverage
ssdCoverage-methods	Standardized SD of the genomic coverage
stdGrid	Compute coverage on user specified genomic regions.
stdGrid-method	Compute coverage on user specified genomic regions.
stdGrid-methods	Compute coverage on user specified genomic regions.
stdPeakLocation	Peak density with respect to closest gene.
stdPeakLocation-method	Peak density with respect to closest gene.
stdPeakLocation-methods	Peak density with respect to closest gene.
tabDuplReads	Detect and filter duplicated reads/sequences.
tabDuplReads-method	Detect and filter duplicated reads/sequences.
tabDuplReads-methods	Detect and filter duplicated reads/sequences.
[-method	Class "gridCover"