Epigenomic tools

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Documentation for package ‘Repitools’ version 1.52.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

A B C D E F G H L M N O P Q R S T W misc

-- A --

abcdDNA	A wrapper for fitting the offset-adjusted ABCD-DNA GLM
absoluteCN	Calculate and Segment Absolute Copy Number from Sequencing Counts
absoluteCN-method	Calculate and Segment Absolute Copy Number from Sequencing Counts
AdjustedCopyEstimate	Container for results of GC adjusted copy number estimation.
AdjustedCopyEstimate-class	Container for results of GC adjusted copy number estimation.
AdjustedCopyEstimate-method	Container for results of GC adjusted copy number estimation.
AffymetrixCdfFile	Placeholder For AffymetrixCdfFile Documentation
AffymetrixCdfFile-class	Placeholder For AffymetrixCdfFile Documentation
AffymetrixCelSet	Placeholder For AffymetrixCelSet Documentation
AffymetrixCelSet-class	Placeholder For AffymetrixCelSet Documentation
annoDF2GR	Convert a 'data.frame' to a 'GRanges'.
annoDF2GR-method	Convert a 'data.frame' to a 'GRanges'.
annoGR2DF	Convert an annotated 'GRanges' to a 'data.frame'.
annoGR2DF-method	Convert an annotated 'GRanges' to a 'data.frame'.
annotationBlocksCounts	Counts the number of sequencing reads within supplied genomic blocks.
annotationBlocksCounts-method	Counts the number of sequencing reads within supplied genomic blocks.
annotationBlocksLookup	Forms a mapping between probe locations and chromosomal blocks (regions).
annotationBlocksLookup-method	Forms a mapping between probe locations and chromosomal blocks (regions).
annotationCounts	Counts the number of sequencing reads surrounding supplied annotations
annotationCounts-method	Counts the number of sequencing reads surrounding supplied annotations
annotationLookup	Forms a mapping between probes on a tiling array and windows surrounding the TSSs of genes.
annotationLookup-method	Forms a mapping between probes on a tiling array and windows surrounding the TSSs of genes.

-- B --

BAM2GRanges	Read in a (list of) BAM file(s) into a GRanges(List) object.
BAM2GRanges-method	Read in a (list of) BAM file(s) into a GRanges(List) object.
BAM2GRangesList	Read in a (list of) BAM file(s) into a GRanges(List) object.
BAM2GRangesList-method	Read in a (list of) BAM file(s) into a GRanges(List) object.
Basic_Statistics	FastQC and associated classes
Basic_Statistics-method	FastQC and associated classes
BayMethList	Class '"BayMethList"'
BayMethList-class	Class '"BayMethList"'
BayMethList-method	Class '"BayMethList"'
binPlots	Create line plots of averaged signal across a promoter
binPlots-method	Create line plots of averaged signal across a promoter
blocks	ChromaResults class
blocks-method	ChromaResults class
blocksStats	Calculate statistics for regions in the genome
blocksStats-method	Calculate statistics for regions in the genome

-- C --

checkProbes	Check Probe Specificity for Some Regions
checkProbes-method	Check Probe Specificity for Some Regions
chr21genes	Positions of Genes on Human Chromosome 21
ChromaBlocks	A function to find areas of enrichment in sequencing data
ChromaBlocks-method	A function to find areas of enrichment in sequencing data
ChromaResults	ChromaResults class
ChromaResults-class	ChromaResults class
chromosomeCNplots	Plot copy number by chromosome
chromosomeCNplots-method	Plot copy number by chromosome
class:ChromaResults	ChromaResults class
class:FastQC	FastQC and associated classes
class:QdnaData	A container for quantitative DNA sequencing data for ABCD-DNA analyses
class:RegionStats	Find Regions of significance in microarray data
class:SequenceQC	FastQC and associated classes
class:SequenceQCSet	FastQC and associated classes
ClusteredScoresList	Container for coverage matrices with clustering results.
ClusteredScoresList-class	Container for coverage matrices with clustering results.
ClusteredScoresList-method	Container for coverage matrices with clustering results.
clusterPlots	Visualisation of tables of feature coverages.
clusterPlots-method	Visualisation of tables of feature coverages.
clusters	Container for coverage matrices with clustering results.
clusters-method	Container for coverage matrices with clustering results.
control	Class '"BayMethList"'
control-method	Class '"BayMethList"'
control<-	Class '"BayMethList"'
control<--method	Class '"BayMethList"'
CopyEstimate	Container for results of fold change copy number estimation.
CopyEstimate-class	Container for results of fold change copy number estimation.
CopyEstimate-method	Container for results of fold change copy number estimation.
cpgBoxplots	Boxplots of intensity, binned by Cpg Density
cpgBoxplots-method	Boxplots of intensity, binned by Cpg Density
cpgDens	Class '"BayMethList"'
cpgDens-method	Class '"BayMethList"'
cpgDens<-	Class '"BayMethList"'
cpgDens<--method	Class '"BayMethList"'
cpgDensityCalc	Calculate CpG Density in a Window
cpgDensityCalc-method	Calculate CpG Density in a Window
cpgDensityPlot	Plot the distribution of sequencing reads CpG densities.
cpgDensityPlot-method	Plot the distribution of sequencing reads CpG densities.
cutoff	ChromaResults class
cutoff-method	ChromaResults class

-- D --

determineOffset

Function to determine the normalising offset f that accounts for the relative sequencing depth.

-- E --

empBayes	Function to calculate prior parameters using empirical Bayes.
enrichmentCalc	Calculate sequencing enrichment
enrichmentCalc-method	Calculate sequencing enrichment
enrichmentPlot	Plot the distribution of sequencing enrichment.
enrichmentPlot-method	Plot the distribution of sequencing enrichment.
expr	Vector of expression differences

-- F --

FastQC-class	FastQC and associated classes
FDRTable	ChromaResults class
FDRTable-method	ChromaResults class
featureBlocks	Make windows for distances around a reference point.
featureBlocks-method	Make windows for distances around a reference point.
featureScores	Get scores at regular sample points around genomic features.
featureScores-method	Get scores at regular sample points around genomic features.
findClusters	Find Clusters Epigenetically Modified Genes
fOffset	Class '"BayMethList"'
fOffset-method	Class '"BayMethList"'
fOffset<-	Class '"BayMethList"'
fOffset<--method	Class '"BayMethList"'

-- G --

GCadjustCopy	Calculate Absolute Copy Number from Sequencing Counts
GCadjustCopy-method	Calculate Absolute Copy Number from Sequencing Counts
GCAdjustParams	Container for parameters for mappability and GC content adjusted absolute copy number estimation.
GCAdjustParams-class	Container for parameters for mappability and GC content adjusted absolute copy number estimation.
GCAdjustParams-method	Container for parameters for mappability and GC content adjusted absolute copy number estimation.
GCbiasPlots	Plot GC content vs. Read Counts Before Normalising, and GC content vs. Copy Estimates After Normalising.
GCbiasPlots-method	Plot GC content vs. Read Counts Before Normalising, and GC content vs. Copy Estimates After Normalising.
gcContentCalc	Calculate The gcContent of a Region
gcContentCalc-method	Calculate The gcContent of a Region
genomeBlocks	Creates bins across a genome.
genomeBlocks-method	Creates bins across a genome.
genQC	Plot Quality Checking Information for Sequencing Data
genQC-method	Plot Quality Checking Information for Sequencing Data
getProbePositionsDf	Translate Affymetrix probe information in a table.
getProbePositionsDf-method	Translate Affymetrix probe information in a table.
getSampleOffsets	Calculates the sample-specific offsets, using the neutral state

-- H --

hcRegions	Masking files for hg19
hyperg2F1_vec	Gaussian hypergeometric function for vectorial arguments

-- L --

length	Class '"BayMethList"'
length-method	Class '"BayMethList"'
length-method	Container for 'featureScores()' output.
loadPairFile	A routine to read Nimblegen tiling array intensities
loadSampleDirectory	A routine to read Nimblegen tiling array intensities

-- M --

makeWindowLookupTable	Using the output of 'annotationLookup', create a tabular storage of the indices
mappabilityCalc	Calculate The Mappability of a Region
mappabilityCalc-method	Calculate The Mappability of a Region
MappabilitySource	Superclass for datatypes that can refer to genome mappability data.
MappabilitySource-class	Superclass for datatypes that can refer to genome mappability data.
maskEmpBayes	Class '"BayMethList"'
maskEmpBayes-method	Class '"BayMethList"'
maskEmpBayes<-	Class '"BayMethList"'
maskEmpBayes<--method	Class '"BayMethList"'
maskOut	Function to mask suspicious regions.
mergeReplicates	Merge GRanges that are of replicate experiments.
mergeReplicates-method	Merge GRanges that are of replicate experiments.
methEst	Class '"BayMethList"'
methEst-method	Class '"BayMethList"'
methEst<-	Class '"BayMethList"'
methEst<--method	Class '"BayMethList"'
methylEst	Function to derive regional methylation estimates.
Mismatches	FastQC and associated classes
Mismatches-method	FastQC and associated classes
MismatchTable	FastQC and associated classes
MismatchTable-method	FastQC and associated classes
multiHeatmap	Superfigure plots

-- N --

names-method	Container for 'featureScores()' output.
names<--method	Container for 'featureScores()' output.
ncontrol	Class '"BayMethList"'
ncontrol-method	Class '"BayMethList"'
nsampleInterest	Class '"BayMethList"'
nsampleInterest-method	Class '"BayMethList"'

-- O --

Overrepresented_sequences	FastQC and associated classes
Overrepresented_sequences-method	FastQC and associated classes

-- P --

Per_base_GC_content	FastQC and associated classes
Per_base_GC_content-method	FastQC and associated classes
Per_base_N_content	FastQC and associated classes
Per_base_N_content-method	FastQC and associated classes
Per_base_sequence_content	FastQC and associated classes
Per_base_sequence_content-method	FastQC and associated classes
Per_base_sequence_quality	FastQC and associated classes
Per_base_sequence_quality-method	FastQC and associated classes
Per_sequence_GC_content	FastQC and associated classes
Per_sequence_GC_content-method	FastQC and associated classes
Per_sequence_quality_scores	FastQC and associated classes
Per_sequence_quality_scores-method	FastQC and associated classes
plotClusters	Plot Scores of Cluster Regions
plotClusters-method	Plot Scores of Cluster Regions
plotQdnaByCN	Plotting the response of qDNA-seq data by CNV
priorTab	Class '"BayMethList"'
priorTab-method	Class '"BayMethList"'
priorTab<-	Class '"BayMethList"'
priorTab<--method	Class '"BayMethList"'
processNDF	Reads in a Nimblegen microarray design file (NDF)
profilePlots	Create line plots of averaged signal across a promoter for gene sets, compared to random sampling.
profilePlots-method	Create line plots of averaged signal across a promoter for gene sets, compared to random sampling.

-- Q --

QdnaData	A container for quantitative DNA sequencing data for ABCD-DNA analyses
QdnaData-class	A container for quantitative DNA sequencing data for ABCD-DNA analyses

-- R --

readFastQC	FastQC and associated classes
regions	ChromaResults class
regions-method	ChromaResults class
regionStats	Find Regions of significance in microarray data
RegionStats-class	Find Regions of significance in microarray data
regionStats-method	Find Regions of significance in microarray data
relativeCN	Calculate and Segment Relative Copy Number From Sequencing Counts
relativeCN-method	Calculate and Segment Relative Copy Number From Sequencing Counts

-- S --

sampleInterest	Class '"BayMethList"'
sampleInterest-method	Class '"BayMethList"'
sampleInterest<-	Class '"BayMethList"'
sampleInterest<--method	Class '"BayMethList"'
samplesList	Short Reads from Cancer and Normal
ScoresList	Container for 'featureScores()' output.
ScoresList-class	Container for 'featureScores()' output.
sequenceCalc	Find occurences of a DNA pattern
sequenceCalc-method	Find occurences of a DNA pattern
SequenceQC-class	FastQC and associated classes
SequenceQCSet	FastQC and associated classes
SequenceQCSet-class	FastQC and associated classes
Sequence_Duplication_Levels	FastQC and associated classes
Sequence_Duplication_Levels-method	FastQC and associated classes
Sequence_Length_Distribution	FastQC and associated classes
Sequence_Length_Distribution-method	FastQC and associated classes
setCNVOffsets	Set the CNVOffsets of a 'QdnaData' object
show-method	Container for results of GC adjusted copy number estimation.
show-method	Class '"BayMethList"'
show-method	ChromaResults class
show-method	Container for coverage matrices with clustering results.
show-method	Container for results of fold change copy number estimation.
show-method	FastQC and associated classes
show-method	A container for quantitative DNA sequencing data for ABCD-DNA analyses
show-method	Container for 'featureScores()' output.
show-method	Find Regions of significance in microarray data
subsetRows	Container for 'featureScores()' output.
subsetRows-method	Container for coverage matrices with clustering results.
subsetRows-method	Container for 'featureScores()' output.
summarizeScores	Subtract scores of different samples.
summarizeScores-method	Subtract scores of different samples.

-- T --

tables	Container for 'featureScores()' output.
tables-method	Container for 'featureScores()' output.

-- W --

windows	Class '"BayMethList"'
windows-method	Class '"BayMethList"'
windows<-	Class '"BayMethList"'
windows<--method	Class '"BayMethList"'
writeWig	Writes sequencing data out into wiggle files
writeWig-method	Writes sequencing data out into wiggle files

-- misc --

[-method	Class '"BayMethList"'
[-method	Container for coverage matrices with clustering results.
[-method	FastQC and associated classes
[-method	Container for 'featureScores()' output.