Package: VariantFiltering 1.49.0

Robert Castelo

VariantFiltering: Filtering of coding and non-coding genetic variants

Filter genetic variants using different criteria such as inheritance model, amino acid change consequence, minor allele frequencies across human populations, splice site strength, conservation, etc.

Authors:Robert Castelo [aut, cre], Dei Martinez Elurbe [ctb], Pau Puigdevall [ctb], Joan Fernandez [ctb]

# Install 'VariantFiltering' in R:

install.packages('VariantFiltering', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rcastelo/variantfiltering/issues

On BioConductor:VariantFiltering-1.49.0(bioc 3.24)VariantFiltering-1.48.0(bioc 3.23)

genetics homo_sapiens annotation snp sequencing highthroughputsequencing

6.13 score 4 stars 21 scripts 1 mentions 86 exports 169 dependencies

Last updated from:7e523589a8. Checks:1 ERROR, 11 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	582
linux-devel-arm64	NOTE	765
linux-devel-x86_64	NOTE	936
source / vignettes	OK	862
linux-release-arm64	NOTE	780
linux-release-x86_64	NOTE	895
macos-release-arm64	NOTE	626
macos-release-x86_64	NOTE	1957
macos-oldrel-arm64	NOTE	570
macos-oldrel-x86_64	NOTE	1972
windows-devel	NOTE	863
windows-release	NOTE	811
windows-oldrel	NOTE	745
wasm-release	OK	545

Exports:aaChangeType aaChangeType<-allVariants annoGroups autosomalDominant autosomalRecessiveHeterozygous autosomalRecessiveHomozygous bamFiles bamFiles<-browseVariants change<-conservedPositions cutoffs cutoffs<-dbSNPpresent dbSNPpresent<-deNovo downstream downstream<-filteredVariants filters filters<-filtersMetadata FiveSpliceSiteVariants genePhylostrata GenePhylostrataDb genePhylostratum humanGenesPhylostrata inheritanceModel MAFpop MAFpop<-maxMAF maxMAF<-minCUFC minCUFC<-minIntronLength minIntronLength<-minPhastCons minPhastCons<-minPhylostratum minPhylostratum<-minScore3ss minScore3ss<-minScore5ss minScore5ss<-naMAF naMAF<-OMIMpresent OMIMpresent<-param readAAradicalChangeMatrix readWm reportVariants resetSamples samples samples<-sequence_variant.gSOXP show softFilterMatrix softFilterMatrix<-sog sortings sortings<-spliceSiteMatricesHuman summary ThreeSpliceSiteVariants unrelatedIndividuals upstream upstream<-variantConsequence variantConsequence<-VariantFilteringParam variantLocation variantLocation<-variantLocations variantType variantType<-width wmFilename wmLocations wmLocations<-wmName wmScore wmStrictLocations wmStrictLocations<-xLinked

Dependencies:abind AnnotationDbi AnnotationFilter AnnotationHub askpass backports base64enc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO biocmake BiocManager BiocParallel BiocVersion biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem checkmate cigarillo cli cluster codetools colorspace commonmark cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray deldir dichromat digest dir.expiry dplyr DT ensembldb evaluate farver fastmap filelock fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GenomicScores ggplot2 glue graph gridExtra gtable Gviz h5mread HDF5Array highr Hmisc hms htmlTable htmltools htmlwidgets httpuv httr httr2 interp IRanges isoband jpeg jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice latticeExtra lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mime nnet openssl otel pillar pkgconfig png prettyunits progress promises ProtGenerics purrr R6 rappdirs RBGL RColorBrewer Rcpp RcppEigen RCurl restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors S7 sass scales Seqinfo shiny shinyjs shinythemes shinyTree snow sourcetools SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex UCSC.utils utf8 VariantAnnotation vctrs viridisLite withr xfun XML xml2 xtable XVector yaml

VariantFiltering: filter coding and non-coding genetic variants

Rendered fromusingVariantFiltering.Rnwusingutils::Sweave

Last update: 2020-09-07
Started: 2014-03-31

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Filtering of coding and non-coding genetic variants	VariantFiltering-package VariantFiltering
Autosomal dominant inheritance analysis	autosomalDominant autosomalDominant,VariantFilteringParam-method
Autosomal recessive inheritance analysis: Heterozygous	autosomalRecessiveHeterozygous autosomalRecessiveHeterozygous,VariantFilteringParam-method
Autosomal recessive inheritance analysis: Homozygous	autosomalRecessiveHomozygous autosomalRecessiveHomozygous,VariantFilteringParam-method
De Novo variants analysis	deNovo deNovo,VariantFilteringParam-method
PhastConsDb class	genePhylostrata genePhylostrata,GenePhylostrataDb-method GenePhylostrataDb GenePhylostrataDb-class genePhylostratum genePhylostratum,GenePhylostrataDb,character-method genePhylostratum,GenePhylostrataDb,missing-method genePhylostratum,GenePhylostrataDb-method humanGenesPhylostrata organism,GenePhylostrataDb-method show,GenePhylostrataDb-method
Read matrix of amino acid radical changes	readAAradicalChangeMatrix
Analysis designed to be applied over a group of unrelated individuals	unrelatedIndividuals unrelatedIndividuals,VariantFilteringParam-method
VariantFiltering parameter class	$,VariantFilteringParam-method class:VariantFilteringParam cutoffs,VariantFilteringParam-method filters,VariantFilteringParam-method names,VariantFilteringParam-method sequence_variant.gSOXP show,VariantFilteringParam-method sog,VariantFilteringParam-method spliceSiteMatricesHuman VariantFilteringParam VariantFilteringParam-class variantLocations
VariantFilteringResults class	allVariants allVariants,VariantFilteringResults-method annoGroups annoGroups,VariantFilteringResults-method bamFiles bamFiles,VariantFilteringResults-method bamFiles<- bamFiles<-,VariantFilteringResults,BamViews-method bamFiles<-,VariantFilteringResults-method browseVariants change change<- change<-,CutoffsList change<-,CutoffsList,ANY,character-method change<-,CutoffsList,ANY,integer-method change<-,CutoffsList,ANY,logical-method change<-,CutoffsList,ANY,numeric-method class:CutoffsList class:VariantFilteringResults cutoffs cutoffs,VariantFilteringResults-method cutoffs<- cutoffs<-,VariantFilteringResults,CutoffsList-method cutoffs<-,VariantFilteringResults,logical-method cutoffs<-,VariantFilteringResults-method CutoffsList CutoffsList-class filteredVariants filteredVariants,VariantFilteringResults-method filters filters,VariantFilteringResults-method filters<- filters<-,VariantFilteringResults-method filtersMetadata filtersMetadata,VariantFilteringParam-method filtersMetadata,VariantFilteringResults-method inheritanceModel inheritanceModel,VariantFilteringResults-method length length,VariantFilteringResults-method param param,VariantFilteringResults-method plot,VariantFilteringResults,ANY-method referenceGenome,VariantFilteringResults-method reportVariants reportVariants,VariantFilteringResults-method resetSamples resetSamples,VariantFilteringResults-method samples samples,VariantFilteringResults-method samples<- samples<-,VariantFilteringResults,character-method samples<-,VariantFilteringResults-method show,CompressedVRangesList-method show,VariantFilteringResults-method show,VariantFilteringResultsUI-method softFilterMatrix,VariantFilteringResults-method softFilterMatrix<-,VariantFilteringResults-method sog sog,VariantFilteringResults-method sortings sortings,VariantFilteringResults-method sortings<- sortings<-,VariantFilteringResults,CutoffsList-method summary,VariantFilteringResults-method VariantFilteringResults VariantFilteringResults-class
FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType	downstream downstream,FiveSpliceSiteVariants-method downstream,ThreeSpliceSiteVariants-method downstream<- downstream<-,FiveSpliceSiteVariants-method downstream<-,ThreeSpliceSiteVariants-method FiveSpliceSiteVariants FiveSpliceSiteVariants-class minIntronLength minIntronLength,FiveSpliceSiteVariants-method minIntronLength,ThreeSpliceSiteVariants-method minIntronLength<- minIntronLength<-,FiveSpliceSiteVariants-method minIntronLength<-,ThreeSpliceSiteVariants-method show,FiveSpliceSiteVariants-method show,ThreeSpliceSiteVariants-method ThreeSpliceSiteVariants ThreeSpliceSiteVariants-class upstream upstream,FiveSpliceSiteVariants-method upstream,ThreeSpliceSiteVariants-method upstream<- upstream<-,FiveSpliceSiteVariants-method upstream<-,ThreeSpliceSiteVariants-method
Weight matrix class	conservedPositions conservedPositions,WeightMatrix-method readWm show,WeightMatrix-method WeightMatrix WeightMatrix-class width,WeightMatrix-method wmFilename wmFilename,WeightMatrix-method wmLocations wmLocations,WeightMatrix-method wmLocations<- wmLocations<-,WeightMatrix,character-method wmLocations<-,WeightMatrix-method wmName wmName,WeightMatrix-method wmScore wmScore,character,character-method wmScore,character,DNAStringSet-method wmScore,WeightMatrix,character-method wmScore,WeightMatrix,DNAStringSet-method wmStrictLocations wmStrictLocations,WeightMatrix-method wmStrictLocations<- wmStrictLocations<-,WeightMatrix,logical-method wmStrictLocations<-,WeightMatrix-method
X-Linked inheritance analysis	xLinked xLinked,VariantFilteringParam-method