Function reference • UMI4Cats

All functions
`dgram()` `dgram<-`() `groupsUMI4C()` `groupsUMI4C<-`() `bait()` `trend()` `resultsUMI4C()`	UMI4C class methods
`makeUMI4C()`	UMI4C-class
`UMI4C2dds()`	UMI4Cats object to DDS object.
`UMI4Cats`	UMI4Cats: A package for analyzing UMI-4C chromatin contact data
`addGrouping()`	Add grouping of UMI-4C samples
`addStepping()`	Add stepping for plotting genes
`alignmentUMI4C()`	UMI4C alignment
`calculateAdaptativeTrend()`	Adaptative smoothing of normalized trend
`calculateDomainogram()`	Create Domainogram
`callInteractions()`	Call significant interactions
`combineUMI4C()`	Combine UMI4C fragments
`contactsUMI4C()`	UMI4C Contacts Processing
`counterUMI4C()`	UMI counting
`createGeneAnnotation()`	Create gene annotation object
`createStatsTable()`	Create stats table
`darken()`	Darken colors
`dds2UMI4C()`	DDS object to UMI4Cats object.
`demultiplexFastq()`	Demultiplex FASTQ files using fastq-multx
`differentialNbinomWaldTestUMI4C()`	Differential UMI4C contacts using DESeq2 Wald Test
`digestGenome()`	Digest reference genome
`.getCache()`	Get BiocFileCache object
`.getSummaryBam()`	Summarize BAM file
`.singleAlignmentUMI4C()`	Align split fastq file
`.singleCounterUMI4C()`	Count UMIs for a given bam file.
`.singlePrepUMI4C()`	Prepar fastq files at a given barcode.
`.singleSplitUMI4C()`	Split fastq files at a given restriction site.
`.smoothMonotone()`	Monotone smoothing of the VST counts
`downloadUMI4CexampleData()`	Download UMI4Cats example datasets
`ex_ciita_umi4c`	Contacs with CIITA promoter
`fisherUMI4C()`	Differential UMI4C contacts using Fisher's Exact test
`formatPlotsUMI4C()`	Format plots for UMI4C
`geoMeanCoordinates()`	Get geometric mean of given coordinates
`getColors()`	Get default colors
`getFactors()`	Get factors fro plotting
`getNormalizationMatrix()`	Get normalization matrix
`getSignInteractions()`	Get significant interactions from a GRangesList
`getViewpointCoordinates()`	Get viewpoint coordinates
`groupSamplesUMI4C()`	Group UMI4C samples
`makeWindowFragments()`	Make windows merging restriction fragments
`nbinomWaldTestUMI4C()`	Differential UMI4C contacts using DESeq2 Wald Test
`plotDifferential()`	Plot differential contacts
`plotDomainogram()`	Plot domainogram
`plotGenes()`	Plot genes
`plotInteractions()`	Plot interactions
`plotInteractionsUMI4C()`	Plot Interactions UMI4C
`plotTrend()`	Plot adaptative smoothen trend
`plotUMI4C()`	Plot UMI4C data
`prepUMI4C()`	Prepare UMI4C data
`smoothMonotoneUMI4C()`	Monotone smoothing of the DDS object VST counts
`splitUMI4C()`	Split UMI4C reads
`statsUMI4C()`	Statistics UMI4C
`theme()`	Theme
`themeXYblank()`	Theme Y blank
`themeXblank()`	Theme X blank
`themeYblank()`	Theme Y blank
`vstUMI4C()`	Variance stabilizing transformation
`waldUMI4C()`	DESeq2 Wald test for differential contacts
`zscoreUMI4C()`	Z-score calculation using residuals of trend and fit UMI4C counts

Reference

All functions