injectSNPs {BSgenome}R Documentation

SNP injection

Description

Inject SNPs from a SNPlocs data package into a genome.

Usage

  available.SNPs(type=getOption("pkgType"))
  injectSNPs(x, SNPlocs_pkgname)

  ## Related utilities
  SNPlocs_pkgname(x)
  SNPcount(x)
  SNPlocs(x, seqname)

Arguments

type Character string indicating the type of package ("source", "mac.binary" or "win.binary") to look for.
x A BSgenome object.
SNPlocs_pkgname The name of a SNPlocs data package containing SNP information for the single sequences contained in x. This package must be already installed (injectSNPs won't try to install it).
seqname The name of a single sequence in x.

Value

available.SNPs returns a character vector containing the names of the SNPlocs data packages that are currently available on the Bioconductor repositories for your version of R/Bioconductor. A SNPlocs data package contains basic SNP information (location and alleles) for a given organism.
injectSNPs returns a copy of the original genome x where some or all of the single sequences were altered by injecting the SNPs defined in the SNPlocs_pkgname package.
SNPlocs_pkgname, SNPcount and SNPlocs return NULL if no SNPs were injected in x (i.e. if x is not a BSgenome object returned by a previous call to injectSNPs). Otherwise SNPlocs_pkgname returns the name of the package from which the SNPs were injected, SNPcount the number of SNPs for each altered sequence in x, and SNPlocs their locations in the sequence whose name is specified by seqname.

Note

injectSNPs, SNPlocs_pkgname, SNPcount and SNPlocs have the side effect to try to load the SNPlocs data package if it's not already loaded.

Author(s)

H. Pages

See Also

BSgenome-class, .inplaceReplaceLetterAt

Examples

  ## Get the list of SNPlocs data packages currently available:
  available.SNPs()

  if (interactive()) {
    ## Make your choice and install with:
    source("http://bioconductor.org/biocLite.R")
    biocLite("SNPlocs.Hsapiens.dbSNP.20071016")
  }

  ## Inject SNPs from dbSNP into the Human genome:
  library(BSgenome.Hsapiens.UCSC.hg18)
  Hsapiens
  SNPlocs_pkgname(Hsapiens)

  HsWithSNPs <- injectSNPs(Hsapiens, "SNPlocs.Hsapiens.dbSNP.20071016")
  HsWithSNPs  # note the extra "with SNPs injected from ..." line
  SNPlocs_pkgname(HsWithSNPs)
  SNPcount(HsWithSNPs)
  SNPlocs(HsWithSNPs, "chr1")

  alphabetFrequency(Hsapiens$chr1)
  alphabetFrequency(HsWithSNPs$chr1)

[Package BSgenome version 1.12.3 Index]