rfPred: Assign rfPred functional prediction scores to a missense variants list

Based on external numerous data files where rfPred scores are pre-calculated on all genomic positions of the human exome, the package gives rfPred scores to missense variants identified by the chromosome, the position (hg19 version), the referent and alternative nucleotids and the uniprot identifier of the protein. Note that for using the package, the user has to be connected on the Internet or to download the TabixFile and index (approximately 3.3 Go).

Author
Fabienne Jabot-Hanin, Hugo Varet and Jean-Philippe Jais
Date of publication
None
Maintainer
Hugo Varet <varethugo@gmail.com>
License
GPL (>=2 )
Version
1.12.0
URLs

View on Bioconductor

Man pages

example_GRanges
Toy example of GRanges object
rfPred-package
Assign functional prediction rfPred scores to human missense...
rfPred_scores-methods
Assign functional prediction rfPred scores to human missense...
rfPred_scores_motor
Motor of 'rfPred_scores'
variant_list_Y
Toy example of data.frame

Files in this package

rfPred/DESCRIPTION
rfPred/NAMESPACE
rfPred/R
rfPred/R/NAMESPACE.r
rfPred/R/example_GRanges.r
rfPred/R/rfPred-package.r
rfPred/R/rfPred_scores-methods.r
rfPred/R/rfPred_scores_motor.r
rfPred/R/variant_list_Y.r
rfPred/build
rfPred/build/vignette.rds
rfPred/data
rfPred/data/example_GRanges.rda
rfPred/data/variant_list_Y.rda
rfPred/inst
rfPred/inst/CITATION
rfPred/inst/NEWS
rfPred/inst/doc
rfPred/inst/doc/vignette.R
rfPred/inst/doc/vignette.Rnw
rfPred/inst/doc/vignette.pdf
rfPred/inst/extdata
rfPred/inst/extdata/chrY_rfPred.txtz
rfPred/inst/extdata/chrY_rfPred.txtz.tbi
rfPred/inst/extdata/example.vcf
rfPred/man
rfPred/man/example_GRanges.Rd
rfPred/man/rfPred-package.Rd
rfPred/man/rfPred_scores-methods.Rd
rfPred/man/rfPred_scores_motor.Rd
rfPred/man/variant_list_Y.Rd
rfPred/src
rfPred/src/outstring.c
rfPred/vignettes
rfPred/vignettes/vignette.Rnw