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. |