Introduction | Quick start | Method overview | Steps before bootstrapping | Import excluded regions | Genome segmentation | Bootstrapping ranges | Assessing properties of bootstrap samples | Bootstrapping and plyranges | Counting the total number of overlaps | Computing the sum of signal value for nearby peaks | Block bootstrapping one region | Visualizing bootstrap types | Session information | References
Package: nullranges 1.19.0
Michael Love
nullranges: Generation of null ranges via bootstrapping or covariate matching
Modular package for generation of sets of ranges representing the null hypothesis. These can take the form of bootstrap samples of ranges (using the block bootstrap framework of Bickel et al 2010), or sets of control ranges that are matched across one or more covariates. nullranges is designed to be inter-operable with other packages for analysis of genomic overlap enrichment, including the plyranges Bioconductor package.
Authors:
nullranges_1.19.0.tar.gz
nullranges_1.19.0.zip(r-4.7)nullranges_1.19.0.zip(r-4.6)nullranges_1.19.0.zip(r-4.5)
nullranges_1.19.0.tgz(r-4.6-any)nullranges_1.19.0.tgz(r-4.5-any)
nullranges_1.19.0.tar.gz(r-4.7-any)nullranges_1.19.0.tar.gz(r-4.6-any)
nullranges_1.19.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
nullranges/json (API)
| # Install 'nullranges' in R: |
| install.packages('nullranges', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/nullranges/nullranges/issues
Pkgdown/docs site:https://nullranges.github.io
On BioConductor:nullranges-1.19.0(bioc 3.24)nullranges-1.18.0(bioc 3.23)
visualizationgenesetenrichmentfunctionalgenomicsepigeneticsgeneregulationgenetargetgenomeannotationannotationgenomewideassociationhistonemodificationchipseqatacseqdnaseseqrnaseqhiddenmarkovmodelbioconductorbootstrapgenomicsmatchingstatistics
Last updated from:3d228ee580. Checks:1 WARNING, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 367 | ||
| linux-devel-x86_64 | OK | 642 | ||
| source / vignettes | OK | 528 | ||
| linux-release-x86_64 | OK | 530 | ||
| macos-release-arm64 | OK | 308 | ||
| macos-oldrel-arm64 | OK | 463 | ||
| windows-devel | OK | 426 | ||
| windows-release | OK | 451 | ||
| windows-oldrel | OK | 390 | ||
| wasm-release | OK | 297 |
Exports:bootRangesBootRangescombnCovcovariatesfocalindicesmakeExampleMatchedDataSetmatchedMatchedmatchedDataMatchedDataFrameMatchedGInteractionsMatchedGRangesmatchitToMatchedmatchRangesmethodoneRegionSegmentoverviewplotCovariateplotPropensityplotSegmentpoolreduceSegmentsegmentDensityshowunmatchedwithReplacement
Dependencies:abindaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitopscigarilloclicodetoolscpp11crayoncurldata.tableDelayedArraydplyrfarverformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesggplot2ggridgesgluegtablehmshttrInteractionSetIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigplyrangesprettyunitsprogressR6RColorBrewerRcppRCurlrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraySummarizedExperimentsystibbletidyselectutf8vctrsviridisLitewithrXMLXVectoryaml
Introduction to bootRanges
Last update: 2025-11-18
Started: 2023-01-03
Matching case study I: CTCF occupancy
Background | Matching with matchRanges() | Assessing quality of matching | Visualizing matching results | Compare CTCF sites | Session information
Last update: 2023-08-02
Started: 2021-06-01
Matching case study II: CTCF orientation
Background | Matching with matchRanges() | Assessing quality of matching | Visualizing matching results | Compare CTCF site orientation | Session information
Last update: 2023-08-02
Started: 2021-06-01
Introduction to matchRanges
Introduction | Terminology | Methodology | Using matchRanges() | Assessing quality of matching | Accessing matched data | Using cobalt to assess balancing | Choosing the method parameter | Nearest-neighbor matching | Rejection sampling | Stratified sampling | Class structure | Implementation details | Session information | References
Last update: 2023-06-23
Started: 2023-01-13
Creating a pool set for matchRanges
Introduction | Obtaining example data | Creating the focal and pool sets | Obtaining the matched set with matchRanges() | Assessing covariate balance
Last update: 2023-01-13
Started: 2022-12-28
Introduction to nullranges
Choice of methods | Related work | Further description of matching and bootstrapping | In other words | Options and features | Consideration of excluded regions | References
Last update: 2022-12-30
Started: 2020-12-22
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Block bootstrap for genomic ranges | bootRanges |
| BootRanges object | BootRanges BootRanges-class |
| Function for creating combinations of covariates | combnCov combnCov,character-method |
| Get covariates from a Matched object | covariates covariates,Matched-method |
| Get focal set from a Matched object | focal focal,MDF_OR_MGR_OR_MGI-method |
| Get indices of matched set | indices indices,Matched-method |
| Function for generating an example matchRanges or Matched dataset | makeExampleMatchedDataSet makeExampleMatchedDataSet,character_OR_missing,logical_OR_missing,character_OR_missing,logical_OR_missing-method |
| Get matched set from a Matched object | matched matched,MDF_OR_MGR_OR_MGI-method |
| Matched objects | Matched Matched-class |
| Get matched data from a Matched object | matchedData matchedData,Matched-method |
| MatchedDataFrame objects | MatchedDataFrame MatchedDataFrame-class |
| MatchedGInteractions objects | MatchedGInteractions MatchedGInteractions-class |
| MatchedGRanges objects | MatchedGRanges MatchedGRanges-class |
| Coerce 'matchit' to 'Matched' object | matchitToMatched matchitToMatched,matchit-method |
| Generate a covariate-matched control set of ranges | matchRanges matchRanges,DF_OR_df_OR_dt,DF_OR_df_OR_dt,formula,character_OR_missing,logical_OR_missing-method matchRanges,GInteractions,GInteractions,formula,character_OR_missing,logical_OR_missing-method matchRanges,GRanges,GRanges,formula,character_OR_missing,logical_OR_missing-method |
| Get matching method used for Matched object | method method,Matched-method |
| Segmentation based on one region | oneRegionSegment |
| Overview of matching quality | overview overview,Matched,numeric_OR_missing-method |
| Covariate plotting for Matched objects | plotCovariate plotCovariate,Matched,character_OR_missing,character_OR_missing,character_OR_missing,character_OR_missing-method |
| Propensity score plotting for Matched objects | plotPropensity plotPropensity,Matched,character_OR_missing,character_OR_missing,character_OR_missing-method |
| Plot genome segmentation | plotSegment |
| Get pool set from a Matched object | pool pool,MDF_OR_MGR_OR_MGI-method |
| Combine nearby regions with same state | reduceSegment |
| Genome segmentation based on feature density | segmentDensity |
| Get unmatched set from a Matched object | unmatched unmatched,MDF_OR_MGR_OR_MGI-method |
| Get replace method | withReplacement withReplacement,Matched-method |
