| 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
basenames 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")