# Summary, annotation and visualization of genomic data

## Documentation for package ‘genomation’ version 1.22.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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.