GenomicDistributions: fast analysis of genomic intervals with Bioconductor

Documentation for package ‘GenomicDistributions’ version 1.2.0

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.requireAndReturn	Checks to make sure a package object is installed, and if so, returns it. If the library is not installed, it issues a warning and returns NULL.
.validateInputs	Checks class of the list of variables. To be used in functions
binBSGenome	Bins a BSgenome object.
binChroms	Naively splits a chromosome into bins
binRegion	Divide regions into roughly equal bins
BSdtToGRanges	Converts a list of data.tables (From BSreadbeds) into GRanges.
calcChromBins	Calculates the distribution of a query set over the genome
calcChromBinsRef	Returns the distribution of query over a reference assembly Given a query set of elements (a GRanges object) and a reference assembly (*e.g. 'hg38'), this will aggregate and count the distribution of the query elements across bins of the reference genome. This is a helper function to create features for common genomes. It is a wrapper of 'calcChromBins', which is more general.
calcCumulativePartitions	Calculates the cumulative distribution of overlaps between query and arbitrary genomic partitions
calcCumulativePartitionsRef	Calculates the cumulative distribution of overlaps for a query set to a reference assembly
calcDinuclFreq	Calculate Dinuclotide content over genomic ranges
calcDinuclFreqRef	Calculate dinucleotide content over genomic ranges
calcExpectedPartitions	Calculates expected partiton overlap based on contribution of each feature (partition) to genome size. Expected and observed overlaps are then compared.
calcExpectedPartitionsRef	Calculates the distribution of observed versus expected overlaps for a query set to a reference assembly
calcFeatureDist	Find the distance to the nearest genomic feature
calcFeatureDistRefTSS	Calculates the distribution of distances from a query set to closest TSS
calcGCContent	Calculate GC content over genomic ranges
calcGCContentRef	Calculate GC content over genomic ranges
calcNeighborDist	Group regions from the same chromosome together and calculate the distances between neighboring regions. Distances are then lumped into a numeric vector.
calcOpenSignal	The function calcOpenSignal takes the input BED file(s) in form of GRanges or GRangesList object, overlaps it with all defined open chromatin regions across cell types and returns a matrix, where each row is the input genomic region (if overlap was found), each column is a cell type, and the value is a normalized ATAC-seq signal.
calcPartitions	Calculates the distribution of overlaps between query and arbitrary genomic partitions
calcPartitionsRef	Calculates the distribution of overlaps for a query set to a reference assembly
calcWidth	Calculate the widths of regions
cellTypeMetadata	Table the maps cell types to tissues and groups
chromSizes_hg19	hg19 chromosome sizes
dtToGr	Converts a data.table (DT) object to a GenomicRanges (GR) object. Tries to be intelligent, guessing chr and start, but you have to supply end or other columns if you want them to be carried into the GR.
dtToGrInternal	Two utility functions for converting data.tables into GRanges objects
exampleOpenSignalMatrix_hg19	A dataset containing a subset of open chromatin regions across all cell types defined by ENCODE for Homo Sapiens hg19
geneModels_hg19	hg38 gene models
genomePartitionList	Create a basic genome partition list of genes, exons, introns, UTRs, and intergenic
GenomicDistributions	Produces summaries and plots of features distributed across genomes
getChromSizes	Returns built-in chrom sizes for a given reference assembly
getChromSizesFromFasta	Get gene models from a remote or local FASTA file
getGeneModels	Returns built-in gene models for a given reference assembly
getGeneModelsFromGTF	Get gene models from a remote or local GTF file
getGenomeBins	Returns bins used in 'calcChromBins' function Given a named vector of chromosome sizes, the function returns GRangesList object with bins for each chromosome.
getReferenceData	Get reference data for a specified assembly
getTssFromGTF	Get transcription start sites (TSSs) from a remote or local GTF file
grToDt	Convert a GenomicRanges into a data.table.
labelCuts	Creates labels based on a discretization definition.
loadBSgenome	Loads BSgenome objects from UCSC-style character vectors.
loadEnsDb	Load selected EnsDb library
neighbordt	Internal helper function to calculate distance between neighboring regions.
nlist	Nathan's magical named list function. This function is a drop-in replacement for the base list() function, which automatically names your list according to the names of the variables used to construct it. It seamlessly handles lists with some names and others absent, not overwriting specified names while naming any unnamed parameters. Took me awhile to figure this out.
plotChromBins	Plot distribution over chromosomes
plotCumulativePartitions	Plot the cumulative distribution of regions in features
plotDinuclFreq	Plot dinuclotide content within region set(s)
plotExpectedPartitions	Produces a barplot showing how query regions of interest are distributed relative to the expected distribution across a given partition list
plotFeatureDist	Plots a histogram of distances to genomic features
plotGCContent	Plots a density distribution of GC vectors Give results from the 'calcGCContent' function, this will produce a density plot
plotNeighborDist	Plot the distances between neighboring regions.The distance in the x axis is log10 transformed for ease of comparison between different regionsets and to account for outliers.
plotOpenSignal	The function plotOpenSignal visualizes the signalMatrix obtained from calcOpenSignal.
plotPartitions	Produces a barplot showing how query regions of interest are distributed across a given partition list
plotQTHist	Plot quantile-trimmed histogram
retrieveFile	Read local or remote file
setB_100	Example BED file read with rtracklayer::import
splitDataTable	Efficiently split a data.table by a column in the table
theme_blank_facet_label	Clear ggplot face label.
TSS_hg19	hg19 TSS locations
vistaEnhancers	Example BED file read with rtracklayer::import