RochePath-class: (Legacy) "RochePath" class representing a Roche (454)...
In ShortRead: FASTQ input and manipulation

Description Objects from the Class Slots Extends Methods Author(s) See Also Examples

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)

experimentPath: character(1) or RochePath pointing to the top-level directory of a Roche experiment.
readPath: character() of directories (typically in experimentPath) containing sequence (read) information. The default selects all directories matching list.files(experimentPath, "run").
qualPath: character() of directories (typically in experimentPath) containing quality information. The default selects all directories matching list.files(experimentPath, "run").
verbose: 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:

readFasta: signature(dirPath = "RochePath", pattern=".\.fna$", sample = 1, run = 1, ...): Read sequences from files matching list.files(dirPath, pattern) (when dirPath="character") or list.files(readPath(dir)[run], pattern)[sample]. The result is a DNAStringSet.
readQual: signature(dirPath = "RochePath", reads=NULL, pattern="\.qual$", 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.
readFastaQual: signature(dirPath = "RochePath", fastaPattern = "\.fna$", qualPattern = "\.qual$", sample = 1, run = 1): read sequences and quality scores into a ShortReadQ instance.
readFastaQual: signature(dirPath = "character", fastaPattern = "\.fna$", qualPattern = "\.qual$", sample = 1, run = 1): wrapper for method above, coercing dirPath to a RochePath via RochePath(dirPath).
readBaseQuality: signature(dirPath = "RochePath", ...): Reads in base and quality information. Currently delegates to readFastaQual, above, but will do more after RochePath supports more file types.
read454: signature(dirPath = "RochePath", ...): Pass arguments on to readFastaQual, documented above.
readPath: signature(object = "RochePath"): return the contents of the readPath slot.
runNames: signature(object = "RochePath"): return the basenames of readPath(object).
RocheSet: signature(path = "RochePath"): create a RocheSet from path.

Additional methods include:

show: signature(object = "RochePath"): Briefly summarize the experiment path locations.
detail: signature(x = "RochePath"): Provide additional detail on the Roche path. All file paths are presented in full.

Michael Lawrence <mflawrence@fhcrc.org>

ExperimentPath.