Epigenomic tools


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Documentation for package ‘Repitools’ version 1.52.0

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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.