denovolyzeR: Statistical Analyses of De Novo Genetic Variants
Version 0.2.0

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.

AuthorJames Ware [aut, cre], Jason Homsy [ctb], Kaitlin Samocha [ctb]
Date of publication2016-08-01 14:55:41
MaintainerJames Ware <j.ware@imperial.ac.uk>
LicenseGPL-3
Version0.2.0
URL http://denovolyzeR.org
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("denovolyzeR")

Getting started

denovolyzeR intro

Popular man pages

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
See all...

All man pages Function index File listing

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

Functions

PermuteMultiHits Man page Source code
autismDeNovos Man page
denovolyze Man page Source code
denovolyzeByClass Man page Source code
denovolyzeByGene Man page Source code
denovolyzeMultiHits Man page Source code
denovolyzeR Man page
denovolyzeR-package Man page
fmrpGenes Man page
parseInput Man page Source code
viewProbabilityTable Man page Source code

Files

inst
inst/CITATION
inst/doc
inst/doc/denovolyzeR_intro.Rmd
inst/doc/denovolyzeR_intro.R
inst/doc/denovolyzeR_intro.html
NAMESPACE
NEWS.md
data
data/autismDeNovos.rda
data/FMRPgenes.rda
R
R/viewProbabilityTable.R
R/PermuteMultiHits.R
R/denovolyzeMultiHits.R
R/sysdata.rda
R/denovolyzeR.doc.R
R/FMRPgenes.doc.R
R/autismDeNovos.doc.R
R/parseInput.R
R/denovolyze.R
vignettes
vignettes/denovolyzeR_intro.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/parseInput.Rd
man/autismDeNovos.Rd
man/denovolyzeR.Rd
man/denovolyzeMultiHits.Rd
man/fmrpGenes.Rd
man/PermuteMultiHits.Rd
man/viewProbabilityTable.Rd
man/denovolyze.Rd
denovolyzeR documentation built on May 20, 2017, 1:41 a.m.

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