wgscores: Discovering genomic gscores

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

Discovering genomic gscores

Description

Functions to discover which genomic scores are present in given genomic ranges through GScores objects.

Usage

## S4 method for signature 'GScores,GenomicRanges'
wgscores(x, ranges, ...)

Arguments

x	A GScores object.
ranges	A GenomicRanges object with genomic ranges where to search for genomic scores.
...	In the call to the wgscores() method one can additionally set the following arguments: 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. 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 wgscores() method is called multiple times.

Details

The method wgscores() takes as first argument a GScores object, previouly loaded from either an annotation package or an AnnotationHub resource; see getGScores() and a GenomicRanges object as a second argument. It will search for which genomic scores fall within the provided genomic ranges and return them in an ordered GenomicRanges object with the scores in the metadata columns.

Value

The method wgscores() returns a GRanges object with the genomic scores in metadata columns named after the corresponding score population name.

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.

See Also

MafDb.1Kgenomes.phase1.hs37d5

Examples

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

  ## lookup allele frequencies for SNP rs1129038, located at 15:28356859 in
  ## GRCh37, a SNP associated to blue and brown eye colors as reported by
  ## Eiberg et al. (Human Genetics, 2008; http://www.ncbi.nlm.nih.gov/pubmed/18172690).
  ## 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.
  ##
  ## for the sake of illustrating this functionality let's create a
  ## GenomicRanges object with the SNP rs1129038 and enlarge its range
  ## by 200nt at each flank.
  snp <- GRanges("15:28356859")
  rngsnp <- flank(snp, width=100, both=TRUE)
  width(rngsnp)

  ## now use this genomic range to search for the rs1129038 SNP
  wgscores(mafdb, rngsnp)

  ## let's illustrate this same functionality for INDELs, starting
  ## from the specific INDEL rs113993960 that leads to the loss of
  ## phenylalanine at amino acid position 508 of the CFTR protein,
  ## commonly referred to as F508del in the CFTR gene, which is
  ## concretely a deletion of four nucleotides at position
  ## 7:117199644 in GRCh37 and enlarge its range by 20nt on each flank.
  indel <- GRanges(seqnames="chr7",
                   ranges=IRanges(start=117199644, width=4))
  rngindel <- flank(indel, width=20, both=TRUE)
  width(rngindel)

  ## now use this genomic range to search for the rs113993960 INDEL
  wgscores(mafdb, rngindel, type="nonsnrs")
}

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