# Epigenomic tools

## Documentation for package ‘Repitools’ version 1.38.0

- 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.