| annotateWithFeature | Function to annotate given GRanges object with a given genomic feature |
| annotateWithFeature-method | Function to annotate given GRanges object with a given genomic feature |
| annotateWithFeatureFlank | Function to annotate a given GRanges object with promoter,exon,intron & intergenic values |
| annotateWithFeatureFlank-method | Function to annotate a given GRanges object with promoter,exon,intron & intergenic values |
| annotateWithFeatures | Annotate given ranges with genomic features |
| annotateWithFeatures-method | Annotate given ranges with genomic features |
| annotateWithGeneParts | Annotate given object with promoter, exon, intron and intergenic regions |
| annotateWithGeneParts-method | Annotate given object with promoter, exon, intron and intergenic regions |
| AnnotationByFeature-class | An S4 class that information on overlap of target features with annotation features |
| AnnotationByGeneParts-class | An S4 class that information on overlap of target features with annotation features |
| AnnotationByGeneParts-method | Get distance to nearest TSS and gene id from AnnotationByGeneParts |
| binMatrix | Bins the columns of a matrix using a user provided function |
| binMatrix-method | Bins the columns of a matrix using a user provided function |
| c.ScoreMatrix | c.ScoreMatrix |
| c.ScoreMatrixList | c.ScoreMatrixList |
| cage | Example CAGE data set. |
| calculateOverlapSignificance | function that calculates the significance of overlaps of two sets of features using randomization |
| calculateOverlapSignificance-method | function that calculates the significance of overlaps of two sets of features using randomization |
| convertBed2Exons | convert a data frame read-in from a bed file to a GRanges object for exons |
| convertBed2Exons-method | convert a data frame read-in from a bed file to a GRanges object for exons |
| convertBed2Introns | convert a data frame read-in from a bed file to a GRanges object for introns |
| convertBed2Introns-method | convert a data frame read-in from a bed file to a GRanges object for introns |
| convertBedDf | convert a data frame read-in from a bed file to a GRanges object |
| convertBedDf-method | convert a data frame read-in from a bed file to a GRanges object |
| cpgi | Example CpG island data set. |
| enrichmentMatrix | Compute an enrichment of IP over control both stored in ScoreMatrix objects |
| enrichmentMatrix-method | Compute an enrichment of IP over control both stored in ScoreMatrix objects |
| enrichmentMatrix-method | Compute an enrichment of IP (stored in ScoreMatrixList object) over control (stored in ScoreMatrix object) |
| enrichmentMatrix-method | Compute an enrichment of IP over control both stored in ScoreMatrixList objects |
| findFeatureComb | Find combitations of genomic features |
| findFeatureComb-method | Find combitations of genomic features |
| genes | Example RefSeq genes data set. |
| getAssociationWithTSS | Get distance to nearest TSS and gene id from AnnotationByGeneParts |
| getAssociationWithTSS, | Get distance to nearest TSS and gene id from AnnotationByGeneParts |
| getAssociationWithTSS,-methods | Get distance to nearest TSS and gene id from AnnotationByGeneParts |
| getAssociationWithTSS-method | Get distance to nearest TSS and gene id from AnnotationByGeneParts |
| getFeatsWithTargetsStats | Get the percentage/count of annotation features overlapping with target features from AnnotationByFeature |
| getFeatsWithTargetsStats-method | Get the percentage/count of annotation features overlapping with target features from AnnotationByFeature |
| getFlanks | Function to get upstream and downstream adjecent regions to a genomic feature such as CpG islands |
| getFlanks-method | Function to get upstream and downstream adjecent regions to a genomic feature such as CpG islands |
| getMembers | Get the membership slot of AnnotationByFeature |
| getMembers-method | Get the membership slot of AnnotationByFeature |
| getRandomEnrichment | get enrichment based on randomized feature overlap |
| getRandomEnrichment-method | get enrichment based on randomized feature overlap |
| getTargetAnnotationStats | Get the percentage of target features overlapping with annotation from AnnotationByFeature |
| getTargetAnnotationStats-method | Get the percentage of target features overlapping with annotation from AnnotationByFeature |
| gffToGRanges | Converts a gff formated data.frame into a GenomicRanges object. The GenomicRanges object needs to be properly formated for the function to work. |
| heatMatrix | Draw a heatmap of a given ScoreMatrix object |
| heatMeta | Heatmap for meta-region profiles |
| heatTargetAnnotation | Plots the percentage of overlapping intervals with genomic features in a heatmap |
| intersectScoreMatrixList | Get common rows from all matrices in a ScoreMatrixList object |
| intersectScoreMatrixList-method | Get common rows from all matrices in a ScoreMatrixList object |
| multiHeatMatrix | Draw multiple heatmaps from a ScoreMatrixList object |
| Ops-method | Ops method for a ScoreMatrix object. It enables to use arithmetic, indicator and logic operations on ScoreMatrix objects. |
| Ops-method | Ops method for a ScoreMatrixList object. It enables to use arithmetic, indicator and logic operations on ScoreMatrixList objects. |
| Ops-method | Ops method for a ScoreMatrixList object. It enables to use arithmetic, indicator and logic operations on ScoreMatrixList objects. |
| Ops-method | Ops method for a ScoreMatrixList object. It enables to use arithmetic, indicator and logic operations on ScoreMatrixList objects. |
| orderBy | Reorder all elements of a ScoreMatrixList to a given ordering vector |
| orderBy-method | Reorder all elements of a ScoreMatrixList to a given ordering vector |
| patternMatrix | Get scores that correspond to k-mer or PWM matrix occurrence for bases in each window |
| patternMatrix-method | Get scores that correspond to k-mer or PWM matrix occurrence for bases in each window |
| plotGeneAnnotation | Plots the percentage of overlapping intervals with genomic features in a heatmap |
| plotMeta | Line plot(s) for meta-region profiles |
| plotTargetAnnotation | Plot annotation categories from AnnotationByGeneParts or AnnotationByFeature |
| plotTargetAnnotation-method | Plot annotation categories from AnnotationByGeneParts or AnnotationByFeature |
| promoters | Example promoter data set. |
| RandomEnrichment-class | An S4 class for storing 'getRandomEnrichment' function results |
| randomizeFeature | function that randomizes the genomic coordinates |
| randomizeFeature-method | function that randomizes the genomic coordinates |
| readBed | Read a BED file and convert it to GRanges. |
| readBroadPeak | A function to read the Encode formatted broad peak file into a GRanges object |
| readFeatureFlank | A function to read-in genomic features and their upstream and downstream adjecent regions such as CpG islands and their shores |
| readFeatureFlank-method | A function to read-in genomic features and their upstream and downstream adjecent regions such as CpG islands and their shores |
| readGeneric | Read a tabular file and convert it to GRanges. |
| readNarrowPeak | A function to read the Encode formatted narrowPeak file into a GRanges object |
| readTranscriptFeatures | Function for reading exon intron and promoter structure from a given bed file |
| readTranscriptFeatures-method | Function for reading exon intron and promoter structure from a given bed file |
| scaleScoreMatrix | Scales the values in the matrix by rows and/or columns |
| scaleScoreMatrix-method | Scales the values in the matrix by rows and/or columns |
| scaleScoreMatrixList | Scale the ScoreMatrixList |
| scaleScoreMatrixList-method | Scale the ScoreMatrixList |
| ScoreMatrix | Get base-pair score for bases in each window |
| ScoreMatrix-class | An S4 class for storing 'ScoreMatrix' function results |
| ScoreMatrix-method | Get base-pair score for bases in each window |
| ScoreMatrixBin | Get bin score for bins on each window |
| ScoreMatrixBin-method | Get bin score for bins on each window |
| ScoreMatrixList | Make ScoreMatrixList from multiple targets |
| ScoreMatrixList-class | An S4 class for storing a set of 'ScoreMatrixList' |
| show-method | show method for some of the genomation classes |
| [-method | Extract method for a ScoreMatrix object. |
| [-method | Extract method for a ScoreMatrixList object. |