GenePhylostrataDb-class: PhastConsDb class

In rcastelo/VariantFiltering: Filtering of coding and non-coding genetic variants

PhastConsDb class

Description

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

Usage

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

Arguments

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.

Details

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.

Value

.

Author(s)

R. Castelo

Source

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

References

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

See Also

phastCons100way.UCSC.hg19

Examples

humanGenesPhylostrata

rcastelo/VariantFiltering documentation built on Oct. 23, 2024, 5:23 p.m.