Summary, annotation and visualization of genomic data

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Documentation for package ‘genomation’ version 1.30.0

• 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.