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