| injectSNPs {BSgenome} | R Documentation |
Inject SNPs from a SNPlocs data package into a genome.
available.SNPs(type=getOption("pkgType"))
injectSNPs(x, SNPlocs_pkgname)
## Related utilities
SNPlocs_pkgname(x)
SNPcount(x)
SNPlocs(x, seqname)
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.
|
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.
injectSNPs, SNPlocs_pkgname, SNPcount and SNPlocs
have the side effect to try to load the SNPlocs data package if it's not
already loaded.
H. Pages
BSgenome-class,
.inplaceReplaceLetterAt
## 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)