gscores: Accessing genomic gscores
In rcastelo/GenomicScores: Infrastructure to work with genomewide position-specific scores

gscores

R Documentation

Accessing genomic gscores

Description

Functions to access genomic gscores through GScores objects.

Usage

## S4 method for signature 'GScores,GenomicRanges'
gscores(x, ranges, ...)
## S4 method for signature 'GScores,character'
gscores(x, ranges, ...)
## S4 method for signature 'GScores'
score(x, ..., simplify=TRUE)

Arguments

`x`	A `GScores` object.
`ranges`	A `GenomicRanges` object with positions from where to retrieve genomic scores, or a character string vector with identifiers associated by the data producer with the genomic scores, e.g., dbSNP 'rs' identifiers in the case of some `MafDb.*` packages.
`...`	In the call to the `gscores`() method one can additionally specify the following optional parameters: `pop:` Character string vector specifying the scores populations to query, when there is more than one. By default, its value is 'defaultPopulation(x)'. Use `populations()` to find out the available scores populations. `type:` Character string specifying the type of genomic position being sought, which can be a single nucleotide range (`snr`), by default, or a `nonsnr` spanning multiple nucleotides. The latter is the case of indel variants in minor allele frequency data. `scores.only:` Flag setting whether only the scores should be returned as a numeric vector (`TRUE`), instead of returning them as a metadata column in a `GRanges` object (`FALSE`, default). `summaryFun:` Function to summarize genomic scores when more than one position is retrieved. By default, this is set to the arithmetic mean, i.e., the `mean()` function. `quantized:` Flag setting whether the genomic scores should be returned quantized (`TRUE`) or dequantized (`FALSE`, default). `ref:` Vector of reference alleles in the form of either a character vector, a `DNAStringSet` object or a `DNAStringSetList` object. This argument is used only when either there are multiple scores per position or `x` is a `MafDb.` package. `alt:` Vector of alternative alleles in the form of either a character vector, a `DNAStringSet` object or a `DNAStringSetList` object. This argument is used only when either there are multiple scores per position or `x` is a `MafDb.` package. `minoverlap:` Integer value passed internally to the function `findOverlaps()` from the `IRanges` package, when querying genomic positions associated with multiple-nucleotide ranges (nonSNRs). By default, `minoverlap=1L`, which assumes that the sought nonSNRs are stored as in `VCF` files, using the nucleotide composition of the reference sequence. This argument is only relevant for genomic scores associated with nonSNRs. `caching:` Flag setting whether genomic 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 `gscores()` method is called multiple times.
`simplify`	Flag setting whether the result should be simplified to a vector (`TRUE`, default) if possible. This happens when scores from a single population are queried.

Details

The method gscores() takes as first argument a GScores object, previouly loaded from either an annotation package or an AnnotationHub resource; see getGScores().

The arguments ref and alt serve two purposes. One, when there are multiple scores per position, such as with CADD or M-CAP, and we want to select a score matching a specific combination of reference and alternate alleles. The other purpose is when the GScores object x is a MafDb.* package, then by providing ref and alt alelles we will get separate frequencies for reference and alternate alleles. The current lossy compression of these values yields a correct assignment for biallelic variants in the corresponding MafDb.* package and an approximation for multiallelic ones.

Value

The method gscores() returns a GRanges object with the genomic scores in a metadata column called score. The method score() returns a numeric vector with the genomic scores.

Author(s)

R. Castelo

References

Puigdevall, P. and Castelo, R. GenomicScores: seamless access to genomewide position-specific scores from R and Bioconductor. Bioinformatics, 18:3208-3210, 2018.

Examples

## one genomic range of width 5
gr1 <- GRanges(seqnames="chr22", IRanges(start=50528591, width=5))
gr1

## five genomic ranges of width 1
gr2 <- GRanges(seqnames="chr22", IRanges(start=50528591:50528596, width=1))
gr2

## accessing genomic gscores from an annotation package
if (require(phastCons100way.UCSC.hg38)) {
  library(GenomicRanges)

  gsco <- phastCons100way.UCSC.hg38
  gsco
  gscores(gsco, gr1)
  score(gsco, gr1)
  gscores(gsco, gr2)
  populations(gsco)
  gscores(gsco, gr2, pop="DP2")
}

if (require(MafDb.1Kgenomes.phase1.hs37d5)) {
  mafdb <- MafDb.1Kgenomes.phase1.hs37d5
  mafdb
  populations(mafdb)

  ## lookup allele frequencies for SNP rs1129038, located at 15:28356859, a
  ## SNP associated to blue and brown eye colors as reported by Eiberg et al.
  ## Blue eye color in humans may be caused by a perfectly associated founder
  ## mutation in a regulatory element located within the HERC2 gene
  ## inhibiting OCA2 expression. Human Genetics, 123(2):177-87, 2008
  ## [http://www.ncbi.nlm.nih.gov/pubmed/18172690]
  gscores(mafdb, GRanges("15:28356859"), pop=populations(mafdb))
  gscores(mafdb, "rs1129038", pop=populations(mafdb))
}

rcastelo/GenomicScores documentation built on May 5, 2024, 11:38 a.m.