RochePath-class | R Documentation |
This class represents the directory location where Roche (454) result files (fasta sequences and qualities) can be found.
Objects from the class are created with the RochePath
constructor:
RochePath(experimentPath = NA_character_,
readPath = experimentPath,
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
:Object of class "character"
, as
described in the constructor, above.
qualPath
:Object of class "character"
, as
described in the constructor, above.
basePath
:Object of class "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 = "RochePath",
pattern=".\.fna$", sample = 1, run = 1, ...)
: Read sequences
from files matching list.files(dirPath, pattern)
(when
dirPath="character"
) or
list.files(readPath(dir)[run], pattern)[sample]
. The
result is a DNAStringSet
.
signature(dirPath = "RochePath", reads=NULL,
pattern="\.qual$", sample=1, run=1, ...)
: Read quality scores
from files matching
list.files(qualPath(dirPath)[run])[sample]
. Non-null
reads
is used as an (optional) template for parsing
quality scores.
signature(dirPath = "RochePath",
fastaPattern = "\.fna$", qualPattern = "\.qual$", sample = 1,
run = 1)
: read sequences and quality scores into a
ShortReadQ
instance.
signature(dirPath = "character",
fastaPattern = "\.fna$", qualPattern = "\.qual$", sample = 1,
run = 1)
: wrapper for method above, coercing dirPath
to a RochePath
via RochePath(dirPath)
.
signature(dirPath = "RochePath", ...)
:
Reads in base and quality information. Currently delegates to
readFastaQual
, above, but will do more after
RochePath
supports more file types.
signature(dirPath = "RochePath", ...)
: Pass
arguments on to readFastaQual
, documented above.
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(x = "RochePath")
: Provide
additional detail on the Roche path. All file paths are presented
in full.
Michael Lawrence <mflawrence@fhcrc.org>
ExperimentPath
.
showClass("RochePath")
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