GenePhylostrataDb-class: PhastConsDb class
Description
Class for storing gene-level conservation information in the form of levels of phylogenetic strata; see Neme and Tautz (2013).Usage
## S3 method for class 'GenePhylostrataDb':
genePhylostrata(object)
## S3 method for class 'GenePhylostrataDb':
genePhylostratum(object, ids)
## S3 method for class 'GenePhylostrataDb':
annotateVariants(annObj, variantsVR, param ,BPPARAM=bpparam("SerialParam"))
## S3 method for class '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.
annObj
A GenePhylostrataDb object.
variantsVR
A VRanges object with the variants to annotate.
BPPARAM
An object of class BiocParallelParam specifying parameters related to
the parallel execution of this function. See function bpparam()
from the BiocParallel package. source
http://genomebiology.com/content/supplementary/1471-2164-14-117-s1.xlsxDetails
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.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