GenePhylostrataDb-class: PhastConsDb class
In VariantFiltering: Filtering of coding and non-coding genetic variants

Description Usage Arguments Details Value Author(s) Source References See Also Examples

Class for storing gene-level conservation information in the form of levels of phylogenetic strata; see Neme and Tautz (2013).

## S4 method for signature 'GenePhylostrataDb'
genePhylostrata(object)
## S4 method for signature 'GenePhylostrataDb'
genePhylostratum(object, ids)
## S4 method for signature 'GenePhylostrataDb'
organism(object)

`object`	A `GenePhylostrataDb` object.
`ids`	A string character vector with the gene identifiers to fetch their phylostrata. These identifiers can be only either Ensembl Gene Identifiers (`ENSGXXXXX`) or Entrez Gene Identifiers.

The GenePhylostrataDb class and associated methods serve the purpose of storing and manipulating gene-level conservation information in the form of levels of phylogenetic strata (Neme and Tautz, 2013). One such objects is created at loading time by the VariantFiltering package with the constructor function GenePhylostrataDb(), and it is called humanGenesPhylostrata.

R. Castelo

http://genomebiology.com/content/supplementary/1471-2164-14-117-s1.xlsx

Neme, R. and Tautz, D. Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution. BMC Genomics, 14:117, 2013

phastCons100way.UCSC.hg19