RochePath-class {ShortRead} | R Documentation |
This class represents the directory location where Roche (454) result files (fasta sequences) can be found.
Objects from the class are created with the RocehPath
constructor:
RochePath(experimentPath = NA_character_,
readPath = .srPath(experimentPath, "run"),
qualPath = readPath, ..., verbose = FALSE)
character(1)
or
RochePath
pointing to the top-level directory
of a Roche experiment.character()
of directories (typically in
experimentPath
) containing sequence (read) information. The
default selects all directories matching
list.files(experimentPath, "run")
.character()
of directories (typically in
experimentPath
) containing quality information. The default
selects all directories matching list.files(experimentPath,
"run")
.logical(1)
indicating whether invalid paths
should be reported interactively.
RocheSet
has the following slots:
readPath
:"character"
, as
described in the constructor, above.qualPath
:"character"
, as
described in the constructor, above.basePath
:"character"
,
containing the experimentPath
.
Class "ExperimentPath"
, directly.
Class ".Roche"
, directly.
Class ".ShortReadBase"
, by class "ExperimentPath", distance 2.
Class ".ShortReadBase"
, by class ".Roche", distance 2.
RochePath
has the following methods or functions defined:
signature(dirPath = "character", pattern=".\.fna$", sample = 1, ...)
:signature(dirPath = "RochePath", pattern=".\.fna$", sample = 1, run, ...)
:
Read sequences from files matching list.files(dirPath,
pattern)
(when dirPath="character"
) or
list.files(readPath(dir)[run], pattern)
, retaining reads
corresponding to sample
. The result is a
DNAStringSet
.
signature(dirPath = "RochePath", pattern="\.qual$", reads=NULL, sample=1, run, ...)
:
Read quality scores from files matching
list.files(qualPath(dirPath)[run])
, corresponding to
sample
. Non-null reads
is used as an (optional)
template for parsing quality scores.
signature(dirPath = "RochePath")
: read
sequences and quality scores into a
ShortReadQ
.signature(object = "RochePath")
: return the
contents of the readPath
slot.signature(object = "RochePath")
: return the
basename
s of readPath(object)
.signature(path = "RochePath")
: create a
RocheSet
from path
.
Additional methods include:
signature(object = "RochePath")
: Briefly
summarize the experiment path locations.signature(object = "RochePath")
: Provide
additional detail on the Roche path. All file paths are presented
in full.Michael Lawrence <mflawrence@fhcrc.org>
showClass("RochePath")