RochePath-class {ShortRead}R Documentation

"RochePath" class representing a Roche (454) experiment location

Description

This class represents the directory location where Roche (454) result files (fasta sequences) can be found.

Objects from the Class

Objects from the class are created with the RocehPath constructor:

RochePath(experimentPath = NA_character_, readPath = .srPath(experimentPath, "run"), 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.

Slots

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.

Extends

Class "ExperimentPath", directly. Class ".Roche", directly. Class ".ShortReadBase", by class "ExperimentPath", distance 2. Class ".ShortReadBase", by class ".Roche", distance 2.

Methods

RochePath has the following methods or functions defined:

readFasta
signature(dirPath = "character", pattern=".\.fna$", sample = 1, ...):
readFasta
signature(dirPath = "RochePath", pattern=".\.fna$", 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.

readQual
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.

read454
signature(dirPath = "RochePath"): read sequences and quality scores into a ShortReadQ.
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(object = "RochePath"): Provide additional detail on the Roche path. All file paths are presented in full.

Author(s)

Michael Lawrence <mflawrence@fhcrc.org>

See Also

ExperimentPath.

Examples

showClass("RochePath")

[Package ShortRead version 1.2.1 Index]