RochePath-class: (Legacy) "RochePath" class representing a Roche (454)...

In Bioconductor/ShortRead: FASTQ input and manipulation

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

Description

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

Objects from the Class

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.

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 = "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.

Author(s)

Michael Lawrence <[e-mail]>

See Also

ExperimentPath.

Examples

showClass("RochePath")

Bioconductor/ShortRead documentation built on Feb. 11, 2024, 8:18 p.m.