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)