\name{BSgenome-class}
\docType{class}
% Classes
\alias{class:BSgenome}
\alias{BSgenome-class}
\alias{BSgenome}
% Accessor methods:
\alias{sourceUrl}
\alias{sourceUrl,BSgenome-method}
\alias{seqnames,BSgenome-method}
\alias{seqlengths,BSgenome-method}
\alias{mseqnames}
\alias{mseqnames,BSgenome-method}
\alias{names,BSgenome-method}
\alias{masknames}
\alias{masknames,BSgenome-method}
% Constructor-like functions and generics:
\alias{BSgenome}
% Standard generic methods:
\alias{show,BSgenome-method}
\alias{length,BSgenome-method}
\alias{[[,BSgenome-method}
\alias{[[<-,BSgenome-method}
\alias{$,BSgenome-method}
\title{BSgenome objects}
\description{
The BSgenome class is a container for the complete genome sequence
of a given organism.
}
\section{Accessor methods}{
In the code snippets below,
\code{x} is a BSgenome object
and \code{name} is the name of a sequence (character-string).
Note that, because the BSgenome class contains the
\code{\link[BSgenome:GenomeDescription-class]{GenomeDescription}} class, then
all the accessor methods for
\code{\link[BSgenome:GenomeDescription-class]{GenomeDescription}}
objects can also be used on \code{x}.
\describe{
\item{\code{sourceUrl(x)}}{
Return the source URL i.e. the permanent URL to the place where the
FASTA files used to produce the sequences contained in \code{x} can
be found (and downloaded).
}
\item{\code{seqnames(x)}}{
Return the index of the single sequences contained in \code{x}.
Each single sequence is stored in a \link[Biostrings]{DNAString}
or \link[Biostrings]{MaskedDNAString} object and typically comes
from a source file (FASTA) with a single record.
The names returned by \code{seqnames(x)} usually reflect the names
of those source files but a common prefix or suffix was eventually
removed in order to keep them as short as possible.
}
\item{\code{seqlengths(x)}}{
Return the lengths of the single sequences contained in \code{x}.
See \code{?`\link[IRanges]{length,XVector-method}`} and
\code{?`\link[Biostrings]{length,MaskedXString-method}`} for
the definition of the length of a \link[Biostrings]{DNAString}
or \link[Biostrings]{MaskedDNAString} object.
Note that the length of a masked sequence
(\link[Biostrings]{MaskedXString} object) is not
affected by the current set of active masks but the \code{nchar}
method for \link[Biostrings]{MaskedXString} objects is.
\code{names(seqlengths(x))} is guaranteed to be identical to
\code{seqnames(x)}.
}
\item{\code{mseqnames(x)}}{
Return the index of the multiple sequences contained in \code{x}.
Each multiple sequence is stored in a
\link[Biostrings]{DNAStringSet} object and typically comes from
a source file (FASTA) with multiple records.
The names returned by \code{mseqnames(x)} usually reflect the names
of those source files but a common prefix or suffix was eventually
removed in order to keep them as short as possible.
}
\item{\code{names(x)}}{
Return the index of all sequences contained in \code{x}.
This is the same as \code{c(seqnames(x), mseqnames(x))}.
}
\item{\code{length(x)}}{
Return the length of \code{x}, i.e., the number of all sequences
that it contains. This is the same as \code{length(names(x))}.
}
\item{\code{x[[name]]}}{
Return sequence (single or multiple) named \code{name}.
No sequence is actually loaded into memory until this is explicitely
requested with a call to \code{x[[name]]} or \code{x$name}.
When loaded, a sequence is kept in a cache. It will be automatically
removed from the cache at garbage collection if it's not in use anymore
i.e. if there are no reference to it (other than the reference stored
in the cache). With \code{options(verbose=TRUE)}, a message is printed
each time a sequence is removed from the cache.
}
\item{\code{x$name}}{
Same as \code{x[[name]]} but \code{name} is not evaluated and
therefore must be a literal character string or a name (possibly
backtick quoted).
}
\item{\code{masknames(x)}}{
The names of the built-in masks that are defined for all the single
sequences. There can be up to 4 built-in masks per sequence. These will
always be (in this order):
(1) the mask of assembly gaps, aka "the AGAPS mask";
(2) the mask of intra-contig ambiguities, aka "the AMB mask";
(3) the mask of repeat regions that were determined by the RepeatMasker
software, aka "the RM mask";
(4) the mask of repeat regions that were determined by the Tandem Repeats
Finder software (where only repeats with period less than or equal to
12 were kept), aka "the TRF mask".
All the single sequences in a given package are guaranteed to have the
same collection of built-in masks (same number of masks and in the same
order).
\code{masknames(x)} gives the names of the masks in this collection.
Therefore the value returned by \code{masknames(x)} is a character vector
made of the first N elements of \code{c("AGAPS", "AMB", "RM", "TRF")},
where N depends only on the BSgenome data package being looked at
(0 <= N <= 4).
The man page for most BSgenome data packages should provide the exact
list and permanent URLs of the source data files that were used to
extract the built-in masks.
For example, if you've installed the BSgenome.Hsapiens.UCSC.hg18 package,
load it and see the Note section in
\code{?`\link[BSgenome.Hsapiens.UCSC.hg18:package]{BSgenome.Hsapiens.UCSC.hg18}`}.
}
}
}
\author{H. Pages}
\seealso{
\code{\link[BSgenome]{available.genomes}},
\link[BSgenome]{GenomeDescription-class},
\link[BSgenome]{BSgenome-utils},
\link[Biostrings]{DNAString-class},
\link[Biostrings]{DNAStringSet-class},
\link[Biostrings]{MaskedDNAString-class},
\code{\link[BSgenome]{getSeq}},
\code{\link[BSgenome]{injectSNPs}},
\link[IRanges]{subseq,XVector-method},
\code{\link[base]{rm}},
\code{\link[base]{gc}}
}
\examples{
## Loading a BSgenome data package doesn't load its sequences
## into memory:
library(BSgenome.Celegans.UCSC.ce2)
## Number of sequences in this genome:
length(Celegans)
## Display a summary of the sequences:
Celegans
## Index of single sequences:
seqnames(Celegans)
## Lengths (i.e. number of nucleotides) of the sequences:
seqlengths(Celegans)
## Load chromosome I from disk to memory (hence takes some time)
## and keep a reference to it:
chrI <- Celegans[["chrI"]] # equivalent to Celegans$chrI
chrI
class(chrI) # a DNAString instance
length(chrI) # with 15080483 nucleotides
## Multiple sequences:
mseqnames(Celegans)
upstream1000 <- Celegans$upstream1000
upstream1000
class(upstream1000) # a DNAStringSet instance
## Character vector containing the description lines of the first
## 4 sequences in the original FASTA file:
names(upstream1000)[1:4]
## ---------------------------------------------------------------------
## PASS-BY-ADDRESS SEMANTIC, CACHING AND MEMORY USAGE
## ---------------------------------------------------------------------
## We want a message to be printed each time a sequence is removed
## from the cache:
options(verbose=TRUE)
gc() # nothing seems to be removed from the cache
rm(chrI, upstream1000)
gc() # chrI and upstream1000 are removed from the cache (they are
# not in use anymore)
options(verbose=FALSE)
## Get the current amount of data in memory (in Mb):
mem0 <- gc()["Vcells", "(Mb)"]
system.time(chrV <- Celegans[["chrV"]]) # read from disk
gc()["Vcells", "(Mb)"] - mem0 # chrV occupies 20Mb in memory
system.time(tmp <- Celegans[["chrV"]]) # much faster! (sequence
# is in the cache)
gc()["Vcells", "(Mb)"] - mem0 # we're still using 20Mb (sequences
# have a pass-by-address semantic
# i.e. the sequence data are not
# duplicated)
## subseq() doesn't copy the sequence data either, hence it is very
## fast and memory efficient (but the returned object will hold a
## reference to chrV):
y <- subseq(chrV, 10, 8000000)
gc()["Vcells", "(Mb)"] - mem0
## We must remove all references to chrV before it can be removed from
## the cache (so the 20Mb of memory used by this sequence are freed).
options(verbose=TRUE)
rm(chrV, tmp)
gc()
## Remember that 'y' holds a reference to chrV too:
rm(y)
gc()
options(verbose=FALSE)
gc()["Vcells", "(Mb)"] - mem0
}
\keyword{methods}
\keyword{classes}