Introduction | Background | Further reading | Setup | Installation | Data | Quick start | DAR analysis | Loading genotype data | Counting alleles | Removing undesired loci | Normalisation of allele counts | Calculating DAR | Assigning DAR values to features | Moderating DGE p-values | Visualisation | The trend in DAR along a chromosome | Comparing DAR between chromosomes | Bibliography | Session information
Package: tadar 1.11.0
Lachlan Baer
tadar: Transcriptome Analysis of Differential Allelic Representation
This package provides functions to standardise the analysis of Differential Allelic Representation (DAR). DAR compromises the integrity of Differential Expression analysis results as it can bias expression, influencing the classification of genes (or transcripts) as being differentially expressed. DAR analysis results in an easy-to-interpret value between 0 and 1 for each genetic feature of interest, where 0 represents identical allelic representation and 1 represents complete diversity. This metric can be used to identify features prone to false-positive calls in Differential Expression analysis, and can be leveraged with statistical methods to alleviate the impact of such artefacts on RNA-seq data.
Authors:
tadar_1.11.0.tar.gz
tadar_1.11.0.zip(r-4.7)tadar_1.11.0.zip(r-4.6)tadar_1.11.0.zip(r-4.5)
tadar_1.11.0.tgz(r-4.6-any)tadar_1.11.0.tgz(r-4.5-any)
tadar_1.11.0.tar.gz(r-4.7-any)tadar_1.11.0.tar.gz(r-4.6-any)
tadar_1.11.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
tadar/json (API)
| # Install 'tadar' in R: |
| install.packages('tadar', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/baerlachlan/tadar/issues
Datasets:
- chr1_genes - Genomic feature example data
- chr1_tt - Differential expression example data
On BioConductor:tadar-1.11.0(bioc 3.24)tadar-1.10.0(bioc 3.23)
sequencingrnaseqsnpgenomicvariationvariantannotationdifferentialexpression
Last updated from:fe09e622bd. Checks:1 WARNING, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 211 | ||
| linux-devel-x86_64 | OK | 559 | ||
| source / vignettes | OK | 376 | ||
| linux-release-x86_64 | OK | 564 | ||
| macos-release-arm64 | OK | 462 | ||
| macos-oldrel-arm64 | OK | 289 | ||
| windows-devel | OK | 463 | ||
| windows-release | OK | 467 | ||
| windows-oldrel | OK | 473 | ||
| wasm-release | OK | 188 |
Exports:assignFeatureDarcountAllelescountsToPropsdarfilterLociflipRangesmodPplotChrDarplotDarECDFreadGenotypesunphaseGT
Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecigarillocliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdplyrensembldbevaluatefarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtableGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2interpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimennetopensslpillarpkgconfigpngprettyunitsprogressProtGenericspurrrR6rappdirsRColorBrewerRcppRcppEigenRCurlrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8VariantAnnotationvctrsviridisLitewithrxfunXMLxml2XVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Assign DAR values to genomic features | assignFeatureDar assignFeatureDar,GRangesList,GRanges-method |
| Genomic feature example data | chr1_genes |
| Differential expression example data | chr1_tt |
| Count alleles within each experimental group | countAlleles countAlleles,GRanges,list-method |
| Convert allele counts to proportions | countsToProps countsToProps,GRangesList-method |
| Calculate Differential Allelic Representation (DAR) | dar dar,GRangesList,matrix-method |
| Filter loci | filterLoci filterLoci,GRangesList-method |
| Convert DAR origin ranges to DAR region ranges, or vice versa | flipRanges flipRanges,GRangesList-method |
| DAR-moderated _p_-values | modP modP,numeric,numeric-method |
| Plot DAR across a chromosome | plotChrDar plotChrDar,GRanges-method |
| Plot the Empirical Cumulative Distribution Function of DAR | plotDarECDF plotDarECDF,GRanges-method |
| Read genotypes from a VCF file | readGenotypes readGenotypes,character-method readGenotypes,TabixFile-method |
| Unphase genotypes | unphaseGT unphaseGT,data.frame-method unphaseGT,matrix-method |
