PhastConsDb-class: PhastConsDb class

Description

Class for annotation packages storing UCSC phastCons conservation scores.

Usage

"annotateVariants"(annObj, variantsVR, param, BPPARAM=bpparam("SerialParam"))
"scores"(object, gpos, summaryFun="mean", coercionFun="as.numeric", caching=TRUE)

Arguments

annObj

A PhastConsDb object.

variantsVR

A VRanges object with the variants to annotate.

param

A VariantFilteringParam-class object.

BPPARAM

An object of class BiocParallelParam specifying parameters related to the parallel execution of this function. See function bpparam() from the BiocParallel package.

object

A PhastConsDb object.

gpos

A GRanges object with positions from where to retrieve phastCons scores.

summaryFun

Function to summarize phastCons scores when more than one position is retrieved. By default is set to the arithmetic mean.

coercionFun

Function to coerce the stored phastCons scores, before the summary function is applied. By default phastCons scores are coerced to real values.

caching

Flag setting whether phastCons scores per chromosome should be kept cached in memory (TRUE, default) or not (FALSE). The latter option minimizes the memory footprint but slows down the performance when the scores() method is called multiple times.

Source

http://genome.ucsc.edu

Details

The PhastConsDb class and associated methods serve the purpose of creating annotation packages that store phastCons nucleotide-level conservation scores from the UCSC Genome Browser. Two such annotation packages are:

phastCons100way.UCSC.hg19: Nucleotide-level phastCons conservation scores from the UCSC Genome Browser calculated from multiple genome alignments from the human genome version hg19 to 99 vertebrate species.

phastCons100way.UCSC.hg38

Nucleotide-level phastCons conservation scores from the UCSC Genome Browser calculated from multiple genome alignments from the human genome version hg38 to 99 vertebrate species.

Examples

Run this code

if (require(phastCons100way.UCSC.hg19)) {
  library(GenomicRanges)

  phastCons100way.UCSC.hg19
  scores(phastCons100way.UCSC.hg19,
         GRanges(seqnames="chr7", IRanges(start=117232380, width=5)))
}