rfPred-package


  The package provides a function which returns the rfPred
  score for a list of non-synonymous missense variants. All
  the rfPred scores are pre-calculated and stored in a
  <code>TabixFile</code> available on a server and which can be
  downloaded for using the package while not connected on
  the Internet. The package does not work without an access
  to the <code>TabixFile</code>. However, a toy example on the
  chromosome Y is available within the package to test the
  <code>rfPred_scores</code> function. curves with numbers of
  subjects at risk, compare data sets, display
  spaghetti-plot, build multi-contingency tables...


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).

Hugo Varet

rfPred

Assign rfPred functional prediction scores to a missense
variants list

rfPred-package function

The package provides a function which returns the rfPred
  score for a list of non-synonymous missense variants. All
  the rfPred scores are pre-calculated and stored in a
  <code>TabixFile</code> available on a server and which can be
  downloaded for using the package while not connected on
  the Internet. The package does not work without an access
  to the <code>TabixFile</code>. However, a toy example on the
  chromosome Y is available within the package to test the
  <code>rfPred_scores</code> function. curves with numbers of
  subjects at risk, compare data sets, display
  spaghetti-plot, build multi-contingency tables...

Assign functional prediction rfPred scores to human missense variants
(random forest method based on SIFT, Polyphen2, PhyloP, LRT and Mutation Taster)

rfPred-package: Assign functional prediction rfPred scores to human missense variants (random forest method based on SIFT, Polyphen2, PhyloP, LRT and Mutation Taster)

Description

Arguments

References