BSgenomeForge {BSgenome} | R Documentation |
A set of functions for making a BSgenome data package.
## Top-level BSgenomeForge function: forgeBSgenomeDataPkg(x, seqs_srcdir=".", masks_srcdir=".", destdir=".", verbose=TRUE) ## Low-level BSgenomeForge functions: forgeSeqlengthsFile(seqnames, prefix="", suffix=".fa", seqs_srcdir=".", seqs_destdir=".", verbose=TRUE) forgeSeqFiles(seqnames, mseqnames=NULL, prefix="", suffix=".fa", seqs_srcdir=".", seqs_destdir=".", verbose=TRUE) forgeMasksFiles(seqnames, nmask_per_seq, seqs_destdir=".", masks_srcdir=".", masks_destdir=".", AGAPSfiles_type="gap", AGAPSfiles_name=NA, AGAPSfiles_prefix="", AGAPSfiles_suffix="_gap.txt", RMfiles_name=NA, RMfiles_prefix="", RMfiles_suffix=".fa.out", TRFfiles_name=NA, TRFfiles_prefix="", TRFfiles_suffix=".bed", verbose=TRUE)
x |
A BSgenomeDataPkgSeed object or the name of a BSgenome data package seed file. See the BSgenomeForge vignette in this package for more information. |
seqs_srcdir, masks_srcdir |
Single strings indicating the path to the source directories i.e. to the directories containing the source data files. Only read access to these directories is needed. See the BSgenomeForge vignette in this package for more information. |
destdir |
A single string indicating the path to the directory where the source tree of the target package should be created. This directory must already exist. See the BSgenomeForge vignette in this package for more information. |
verbose |
TRUE or FALSE .
|
seqnames, mseqnames |
A character vector containing the names of the single (for seqnames )
and multiple (for mseqnames ) sequences to forge.
See the BSgenomeForge vignette in this package for more information.
|
prefix, suffix |
See the BSgenomeForge vignette in this package for more information,
in particular the description of the seqfiles_prefix and
seqfiles_suffix fields of a BSgenome data package seed file.
|
seqs_destdir, masks_destdir |
During the forging process the source data files are converted into
serialized Biostrings objects. seqs_destdir and masks_destdir
must be single strings indicating the path to the directories where these
serialized objects should be saved.
These directories must already exist.
|
nmask_per_seq |
A single integer indicating the desired number of masks per sequence. See the BSgenomeForge vignette in this package for more information. |
AGAPSfiles_type, AGAPSfiles_name, AGAPSfiles_prefix, AGAPSfiles_suffix,
RMfiles_name, RMfiles_prefix, RMfiles_suffix,
TRFfiles_name, TRFfiles_prefix, TRFfiles_suffix |
These arguments are named accordingly to the corresponding fields of a BSgenome data package seed file. See the BSgenomeForge vignette in this package for more information. |
These functions are intended for Bioconductor users who want to make a new
BSgenome data package, not for regular users of these packages.
See the BSgenomeForge vignette in this package
(vignette("BSgenomeForge")
) for an extensive coverage
of this topic.
H. Pages
forgeSeqFiles("chrM", prefix="ce2", suffix=".fa", seqs_srcdir=system.file("extdata", package="BSgenome"), seqs_destdir=tempdir()) load(file.path(tempdir(), "chrM.rda")) chrM