Package: GenomicInteractions 1.39.0

Liz Ing-Simmons

GenomicInteractions: Utilities for handling genomic interaction data

Utilities for handling genomic interaction data such as ChIA-PET or Hi-C, annotating genomic features with interaction information, and producing plots and summary statistics.

Authors:Harmston, N., Ing-Simmons, E., Perry, M., Baresic, A., Lenhard, B.

# Install 'GenomicInteractions' in R:

install.packages('GenomicInteractions', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/computationalregulatorygenomicsicl/genomicinteractions/issues

Datasets:

hg19.refseq.transcripts - Human Refseq transcripts from chr 17-18
hic_example_data - Example HiC dataset
mm9_refseq_promoters - Mouse Refseq promoters from chr 14-15
thymus_enh - Putative enhancers from mouse thymus data

On BioConductor:GenomicInteractions-1.39.0(bioc 3.20)GenomicInteractions-1.38.0(bioc 3.19)

bioconductor-package

52 exports 2.09 score 149 dependencies 6 dependents 10 mentions

Last updated 2 months agofrom:56932e965f

Exports:anchorOne anchorTwo annotateInteractions annotateRegions annotationFeatures asBED availableDisplayPars calculateDistances categoriseInteractions chromosome countsBetweenAnchors description description<-end export.bed12 export.bedpe export.chiasig export.igraph GenomicInteractions get_binom_ligation_threshold get_self_ligation_threshold interactionCounts interactionCounts<-InteractionTrack is.cis is.dd is.dt is.pd is.pp is.pt is.trans is.tt isInteractionType makeGenomicInteractionsFromFile name name<-plotAvgViewpoint plotCisTrans plotCounts plotDists plotInteractionAnnotations plotSummaryStats plotViewpoint removeDups resetAnnotations start subset subsetByFeatures summariseByFeaturePairs summariseByFeatures updateObject viewPoint

Dependencies:abind AnnotationDbi AnnotationFilter askpass backports base64enc BH Biobase BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem checkmate cli cluster codetools colorspace cpp11 crayon curl data.table DBI dbplyr DelayedArray deldir dichromat digest dplyr ensembldb evaluate fansi farver fastmap filelock fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gridExtra gtable Gviz highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 igraph InteractionSet interp IRanges isoband jpeg jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice latticeExtra lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme nnet openssl pillar pkgconfig plogr png prettyunits progress ProtGenerics purrr R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl restfulr Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors sass scales snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite withr xfun XML xml2 XVector yaml zlibbioc

Package Vignette for Genomic Interactions: ChIA-PET data

Malcolm Perry

Rendered fromchiapet_vignette.rmdusingknitr::rmarkdownon Jun 19 2024.

Last update: 2020-04-13
Started: 2014-10-03

HiC vignette for GenomicInteractions package

Liz Ing-Simmons

Rendered fromhic_vignette.Rmdusingknitr::rmarkdownon Jun 19 2024.

Last update: 2020-04-13
Started: 2014-10-03

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
GenomicInteractions	GenomicInteractions-package
Function to read in processed Hi-C interaction data generated by hiclib	.importHicLib
Function to read in processed Hi-C interaction data generated by HOMER	.importHomer
Function to process names relating to interactions stored in bed12 formats.	.processChiapetName
Function to read in interaction-data stored in a BAM file	.readBam
Function to read in interaction-data stored in a pair of BAM files	.readTwoBams
Function to validate tabular input	.validateInput
Annotate the interactions in a GInteractions object	annotateInteractions annotateInteractions,GInteractions,list-method
Annotate regions	annotateRegions annotateRegions,GInteractions,character,vector-method
Coerce to BED structure	asBED,GInteractions-method
The default display parameters for a track object class can be queries using the availableDisplayPars function.	availableDisplayPars
Calculate interaction distances	calculateDistances calculateDistances,GInteractions-method
Get the numbers of interaction types existing in your data	categoriseInteractions
Summarise interactions between defined anchors	countsBetweenAnchors countsBetweenAnchors,GInteractions,GRanges-method
Export interactions in BED12 format.	export.bed12 export.bed12,GInteractions-method
Export interactions in BED Paired-End format.	export.bedpe export.bedpe,GInteractions-method
Export interactions in a BEDPE-like format for use with ChiaSig	export.chiasig export.chiasig,GInteractions-method
Export interactions to an igraph object.	export.igraph export.igraph,GInteractions-method
Function to create a GenomicInteractions object	GenomicInteractions GenomicInteractions,ANY,ANY,ANY-method GenomicInteractions,GInteractions,ANY,ANY-method GenomicInteractions,GInteractions,numeric,ANY-method GenomicInteractions,GRanges,GRanges,GenomicRanges_OR_missing-method GenomicInteractions,GRanges,GRanges,numeric-method GenomicInteractions,missing,missing,GenomicRanges_OR_missing-method GenomicInteractions,numeric,numeric,GRanges-method
A S4 class to represent interactions between genomic regions.	GenomicInteractions-class
get self ligation threshold with binomial test	get_binom_ligation_threshold
Get self ligation threshold with SD method from Heidari et al	get_self_ligation_threshold
Functions to access data held in a GenomicInteractions object.	anchorOne anchorOne,GInteractions-method anchorTwo anchorTwo,GInteractions-method annotationFeatures annotationFeatures,GInteractions-method description,GInteractions-method getters interactionCounts interactionCounts,GInteractions-method name name,GInteractions-method
Human Refseq transcripts from chr 17-18	hg19.refseq.transcripts
Example HiC dataset	hic_example_data
Constructor to create an InteractionTrack object	InteractionTrack
A class to hold chromatin interaction data for a specific genomic region	chromosome,InteractionTrack-method end,InteractionTrack-method InteractionTrack-class start,InteractionTrack-method subset,InteractionTrack-method
Interaction Type Helpers	InteractionHelpers is.cis is.cis,GInteractions-method is.dd is.dd,GInteractions-method is.dt is.dt,GInteractions-method is.pd is.pd,GInteractions-method is.pp is.pp,GInteractions-method is.pt is.pt,GInteractions-method is.trans is.trans,GInteractions-method is.tt is.tt,GInteractions-method isInteractionType isInteractionType,GInteractions-method
Function to create GenomicInteraction objects from a file	makeGenomicInteractionsFromFile
Mouse Refseq promoters from chr 14-15	mm9_refseq_promoters
Plot coverage around a set of virtual 4C viewpoints	plotAvgViewpoint
Plots the percentages of cis and trans interactions for a GInteractions object as a donut plot.	plotCisTrans
Plot a bar chart of the number of interactions supported by different numbers of reads in your data.	plotCounts
Plots a histogram of interaction distances for a GInteractions Object	plotDists
Plot a donut plot of interaction types for an annotated GInteractions object	plotInteractionAnnotations
Plot summary statistics for a GInteractions object	plotSummaryStats
Plot coverage around a virtual 4C viewpoint	plotViewpoint
Remove all but one occurences of a duplicated interaction	removeDups
Reset annotations made to a GInteractions object	resetAnnotations resetAnnotations,GInteractions-method
Tests whether anchors have the same strand.	sameStrand
Functions to set data held in a GInteractions object.	description<-,GInteractions,ANY-method interactionCounts<- interactionCounts<-,GInteractions-method name<- name<-,GInteractions-method setters
Subset a GInteractions object by features	subsetByFeatures subsetByFeatures,GInteractions,character,character-method subsetByFeatures,GInteractions,GRanges,missing-method subsetByFeatures,GInteractions,GRangesList,missing-method
Return the total number of interactions in a GInteractions GIObject	sum,GInteractions-method
Summarise the number of interactions between two sets of features.	summariseByFeaturePairs summariseByFeaturePairs,GInteractions-method
Summary statistics of interactions for a given feature set	summariseByFeatures summariseByFeatures,GInteractions-method
Putative enhancers from mouse thymus data	thymus_enh
updateObject method for GenomicInteractions 1.3.7 and earlier	updateObject,GenomicInteractions-method
Virtual 4C viewpoint	viewPoint