injectSNPs: SNP injection

In Bioconductor/BSgenome: Software infrastructure for efficient representation of full genomes and their SNPs

SNP injection

Description

Inject SNPs from a SNPlocs data package into a genome.

Usage

injectSNPs(x, snps)

SNPlocs_pkgname(x)

## S4 method for signature 'BSgenome'
snpcount(x)
## S4 method for signature 'BSgenome'
snplocs(x, seqname, ...)

## Related utilities
available.SNPs(type=getOption("pkgType"))
installed.SNPs()

Arguments

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

Value

injectSNPs returns a copy of the original genome x where some or all of the single sequences from x are altered by injecting the SNPs stored in snps. The SNPs in the altered genome are represented by an IUPAC ambiguity code at each SNP location.

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.

available.SNPs returns a character vector containing the names of the SNPlocs and XtraSNPlocs data packages that are currently available on the Bioconductor repositories for your version of R/Bioconductor. A SNPlocs data package contains basic information (location and alleles) about the known molecular variations of class snp for a given organism. A XtraSNPlocs data package contains information about the known molecular variations of other classes (in-del, heterozygous, microsatellite, named-locus, no-variation, mixed, multinucleotide-polymorphism) for a given organism. Only SNPlocs data packages can be used for SNP injection for now.

installed.SNPs returns a character vector containing the names of the SNPlocs and XtraSNPlocs data packages that are already installed.

Note

injectSNPs, SNPlocs_pkgname, snpcount and snplocs have the side effect to try to load the SNPlocs data package that was specified thru the snps argument if it's not already loaded.

Author(s)

H. Pagès

See Also

BSgenome-class, IUPAC_CODE_MAP, injectHardMask, letterFrequencyInSlidingView, .inplaceReplaceLetterAt

Examples

## What SNPlocs data packages are already installed:
installed.SNPs()

## What SNPlocs data packages are available:
available.SNPs()

if (interactive()) {
  ## Make your choice and install with:
  if (!require("BiocManager"))
    install.packages("BiocManager")
  BiocManager::install("SNPlocs.Hsapiens.dbSNP144.GRCh38")
}

## Inject SNPs from dbSNP into the Human genome:
library(BSgenome.Hsapiens.UCSC.hg38.masked)
genome <- BSgenome.Hsapiens.UCSC.hg38.masked
SNPlocs_pkgname(genome)

genome2 <- injectSNPs(genome, "SNPlocs.Hsapiens.dbSNP144.GRCh38")
genome2  # note the extra "with SNPs injected from ..." line
SNPlocs_pkgname(genome2)
snpcount(genome2)
head(snplocs(genome2, "chr1"))

alphabetFrequency(genome$chr1)
alphabetFrequency(genome2$chr1)

## Find runs of SNPs of length at least 25 in chr1. Might require
## more memory than some platforms can handle (e.g. 32-bit Windows
## and maybe some Mac OS X machines with little memory):
is_32bit_windows <- .Platform$OS.type == "windows" &&
                    .Platform$r_arch == "i386"
is_macosx <- substr(R.version$os, start=1, stop=6) == "darwin"
if (!is_32bit_windows && !is_macosx) {
    chr1 <- injectHardMask(genome2$chr1)
    ambiguous_letters <- paste(DNA_ALPHABET[5:15], collapse="")
    lf <- letterFrequencyInSlidingView(chr1, 25, ambiguous_letters)
    sl <- slice(as.integer(lf), lower=25)
    v1 <- Views(chr1, start(sl), end(sl)+24)
    v1
    max(width(v1))  # length of longest SNP run
}

Bioconductor/BSgenome documentation built on Oct. 31, 2024, 10:46 p.m.