denovolyzeR: Statistical Analyses of De Novo Genetic Variants

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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.

Author
James Ware [aut, cre], Jason Homsy [ctb], Kaitlin Samocha [ctb]
Date of publication
2016-08-01 14:55:41
Maintainer
James Ware <j.ware@imperial.ac.uk>
License
GPL-3
Version
0.2.0
URLs

View on CRAN

Man pages

autismDeNovos
de novo variants found in 1,078 autism trios
denovolyze
Evaluates burden of _de novo_ variation against expectation
denovolyzeMultiHits
Determine significance of genes with multiple _de novos_
denovolyzeR
A package for the analysis of _de novo_ sequencing variants
fmrpGenes
FMRP genes
parseInput
Checks input for errors
PermuteMultiHits
Permutes x variants across a genelist, and counts genes with...
viewProbabilityTable
Displays underlying _de novo_ probability tables

Files in this package

denovolyzeR
denovolyzeR/inst
denovolyzeR/inst/CITATION
denovolyzeR/inst/doc
denovolyzeR/inst/doc/denovolyzeR_intro.Rmd
denovolyzeR/inst/doc/denovolyzeR_intro.R
denovolyzeR/inst/doc/denovolyzeR_intro.html
denovolyzeR/NAMESPACE
denovolyzeR/NEWS.md
denovolyzeR/data
denovolyzeR/data/autismDeNovos.rda
denovolyzeR/data/FMRPgenes.rda
denovolyzeR/R
denovolyzeR/R/viewProbabilityTable.R
denovolyzeR/R/PermuteMultiHits.R
denovolyzeR/R/denovolyzeMultiHits.R
denovolyzeR/R/sysdata.rda
denovolyzeR/R/denovolyzeR.doc.R
denovolyzeR/R/FMRPgenes.doc.R
denovolyzeR/R/autismDeNovos.doc.R
denovolyzeR/R/parseInput.R
denovolyzeR/R/denovolyze.R
denovolyzeR/vignettes
denovolyzeR/vignettes/denovolyzeR_intro.Rmd
denovolyzeR/MD5
denovolyzeR/build
denovolyzeR/build/vignette.rds
denovolyzeR/DESCRIPTION
denovolyzeR/man
denovolyzeR/man/parseInput.Rd
denovolyzeR/man/autismDeNovos.Rd
denovolyzeR/man/denovolyzeR.Rd
denovolyzeR/man/denovolyzeMultiHits.Rd
denovolyzeR/man/fmrpGenes.Rd
denovolyzeR/man/PermuteMultiHits.Rd
denovolyzeR/man/viewProbabilityTable.Rd
denovolyzeR/man/denovolyze.Rd