All functions

BSdtToGRanges()

Converts a list of data.tables (From BSreadbeds) into GRanges.

GenomicDistributions

Produces summaries and plots of features distributed across genomes

TSS_hg19

hg19 TSS locations

binBSGenome()

Bins a BSgenome object.

binChroms()

Naively splits a chromosome into bins

binRegion()

Divide regions into roughly equal bins

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

.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

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

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.

vistaEnhancers

Example BED file read with rtracklayer::import