RochePath-class {ShortRead} | R Documentation

## (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 `basename`s 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 <mflawrence@fhcrc.org>

### See Also

`ExperimentPath`.

### Examples

    showClass("RochePath")

[Package ShortRead version 1.48.0 Index]