# GenomicDistributions: fast analysis of genomic intervals with Bioconductor

## Documentation for package ‘GenomicDistributions’ version 1.14.0

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

## Help Pages

.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.

calcChromBinsRefSlow

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
calcNearestNeighbors | Group regions from the same chromosome together and compute the distance of a region to its nearest neighbor. Distances are then lumped into a numeric vector.
calcNeighborDist | Group regions from the same chromosome together and calculate the distances of a region to its upstream and downstream neighboring regions. Distances are then lumped into a numeric vector.
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
calcSummarySignal | The function calcSummarySignal takes the input BED file(s) in form of GRanges or GRangesList object, overlaps it with all defined open chromatin regions across conditions (e.g. cell types) and returns a matrix, where each row is the input genomic region (if overlap was found), each column is a condition, and the value is a meam signal from regions where overlap was found.
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 from regions to their upstream/downstream neighbors or nearest neighbors. Distances can be passed as either raw bp or corrected for the number of regions (log10(obs/exp)), but this has to be specified in the function parameters.
plotPartitions | Produces a barplot showing how query regions of interest are distributed across a given partition list
plotQTHist | Plot quantile-trimmed histogram
plotSummarySignal | The function plotSummarySignal visualizes the signalSummaryMatrix obtained from 'calcSummarySignal'.
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