Statistics for de novo variant analysis | Introduction | Installation | Example analysis | Overall de novo burden | Genes containing multiple de novos | Do any individual genes contain more de novos than expected | Geneset analysis | Other functions
Package: denovolyzeR 0.2.0
denovolyzeR: Statistical Analyses of De Novo Genetic Variants
An integrated toolset for the analysis of de novo (sporadic) genetic sequence variants. denovolyzeR implements a mutational model that estimates the probability of a de novo genetic variant arising in each human gene, from which one can infer the expected number of de novo variants in a given population size. Observed variant frequencies can then be compared against expectation in a Poisson framework. denovolyzeR provides a suite of functions to implement these analyses for the interpretation of de novo variation in human disease.
Authors:
denovolyzeR_0.2.0.tar.gz
denovolyzeR_0.2.0.zip(r-4.7-any)denovolyzeR_0.2.0.zip(r-4.6-any)denovolyzeR_0.2.0.zip(r-4.5-any)
denovolyzeR_0.2.0.tgz(r-4.6-any)denovolyzeR_0.2.0.tgz(r-4.5-any)
denovolyzeR_0.2.0.tar.gz(r-4.7-any)denovolyzeR_0.2.0.tar.gz(r-4.6-any)
denovolyzeR_0.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
denovolyzeR/json (API)
| # Install 'denovolyzeR' in R: |
| install.packages('denovolyzeR', repos = c('https://jamesware.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/jamesware/denovolyzer/issues
Datasets:
- autismDeNovos - De novo variants found in 1,078 autism trios
- fmrpGenes - FMRP genes
Last updated from:badc99f8d6. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 141 | ||
| source / vignettes | OK | 182 | ||
| linux-release | OK | 142 | ||
| macos-release | OK | 113 | ||
| macos-oldrel | OK | 132 | ||
| windows-devel | OK | 82 | ||
| windows-release | OK | 76 | ||
| windows-oldrel | OK | 93 | ||
| wasm-release | OK | 99 |
Exports:denovolyzedenovolyzeByClassdenovolyzeByGenedenovolyzeMultiHitsviewProbabilityTable
Dependencies:clidplyrgenericsgluelifecyclemagrittrpillarpkgconfigplyrR6Rcppreshape2rlangstringistringrtibbletidyselectutf8vctrswithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| de novo variants found in 1,078 autism trios | autismDeNovos |
| Evaluates burden of _de novo_ variation against expectation | denovolyze denovolyzeByClass denovolyzeByGene |
| Determine significance of genes with multiple _de novos_ | denovolyzeMultiHits |
| A package for the analysis of _de novo_ sequencing variants | denovolyzeR-package denovolyzeR |
| FMRP genes | fmrpGenes |
| Checks input for errors | parseInput |
| Permutes x variants across a genelist, and counts genes with multiple hits | PermuteMultiHits |
| Displays underlying _de novo_ probability tables | viewProbabilityTable |