BSgenome-class {BSgenome} | R Documentation |
A container for the complete genome sequence of a given specie.
[TODO: Put some details here]
In the code snippets below,
x
is a BSgenome object
and name
is the name of a chromosome (character-string).
names(x)
:
Returns the index of BStringViews objects
contained in x
.
Each BStringViews object in x
was created
from a single FASTA file. The names returned by names(x)
are usually the names of those source files but eventually
a common prefix or suffix was removed in order to keep them as
short as possible.
length(x)
:
Returns the length of x
, i.e., the number
of BStringViews objects that it contains.
This is the same as length(names(x))
.
x[[name]]
:
[TODO: Document me]
x$name
:
[TODO: Document me]
In the code snippets below,
x
is a BSgenome object
and name
is the name of a chromosome (character-string).
unload(x, name)
:
[TODO: Document me]
H. Pages
matchPattern, BStringViews, DNAString
library(BSgenome.Celegans.UCSC.ce2) length(Celegans) Celegans ## Access chromosome V (BStringViews object) with Celegans[["chrV"]] ## or with Celegans$chrV ## Note that the chromosome V data are not loaded into memory until the ## first time you try to access them (what gets loaded is the serialized ## BStringViews instance stored in the "chrV.rda" file) ## To unload chromosome V (if you need to free some memory) unload(Celegans, "chrV") ## Note that assignment of BStringViews objects does NOT copy the data c <- Celegans[["chrV"]] ## But then, clean unloading is a bit more complicated unload(Celegans, "chrV") remove(c) ## More generally, you need to keep track of all BStringViews objects ## referencing the same data if you want to be able to unload these data ## from memory