A B C D E F G H L M N O P Q R S T W misc
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. |
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 |
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 |
determineOffset | Function to determine the normalising offset f that accounts for the relative sequencing depth. |
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 |
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"' |
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 |
hcRegions | Masking files for hg19 |
hyperg2F1_vec | Gaussian hypergeometric function for vectorial arguments |
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 |
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 |
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"' |
Overrepresented_sequences | FastQC and associated classes |
Overrepresented_sequences-method | FastQC and associated classes |
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. |
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 |
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 |
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. |
tables | Container for 'featureScores()' output. |
tables-method | Container for 'featureScores()' output. |
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 |
[-method | Class '"BayMethList"' |
[-method | Container for coverage matrices with clustering results. |
[-method | FastQC and associated classes |
[-method | Container for 'featureScores()' output. |