SolexaPath-class {ShortRead} | R Documentation

## (Legacy) "SolexaPath" class representing a standard output file hierarchy

### Description

Solexa produces a hierarchy of output files. The content of the hierarchy varies depending on analysis options. This class represents a standard class hierarchy, constructed by searching a file hierarchy for appropriately named directories.

### Objects from the Class

Objects from the class are created by calls to the constructor:

`SolexaPath(experimentPath, dataPath=.solexaPath(experimentPath, "Data"), scanPath=.solexaPath(dataPath, "GoldCrest"), imageAnalysisPath=.solexaPath(dataPath, "^(C|IPAR)"), baseCallPath=.solexaPath(imageAnalysisPath, "^Bustard"), analysisPath=.solexaPath(baseCallPath, "^GERALD"), ..., verbose=FALSE)`

experimentPath

  `character(1)` object pointing to the top-level directory of a Solexa run, e.g., `/home/solexa/user/080220_HWI-EAS88_0004`. This is the only required argument

dataPath

  (optional) Solexa ‘Data’ folder .

scanPath

  (optional) Solexa GoldCrest image scan path.

imageAnalysisPath

  (optional) Firecrest image analysis path.

baseCallPath

  (optional) Bustard base call path.

analysisPath

  (optional) Gerald analysis pipeline path.

...

  Additional arguments, unused by currently implemented methods.

verbose=FALSE

  (optional) logical vector which, when `TRUE` results in warnings if paths do not exist.

All paths must be fully-specified.

### Slots

`SolexaPath` has the following slots, containing either a fully specified path to the corresponding directory (described above) or `NA` if no appropriate directory was discovered.

`basePath`

  See `experimentPath`, above.

`dataPath`

  See above.

`scanPath`

  See above.

`imageAnalysisPath`

  See above.

`baseCallPath`

  See above.

`analysisPath`

  See above.

### Extends

Class `".Solexa"`, directly. Class `".ShortReadBase"`, by class ".Solexa", distance 2.

### Methods

Transforming methods include:

readIntensities

  `signature(dirPath = "SolexaPath", pattern=character(0), run, ...)`:

  Use `imageAnalysisPath(sp)[run]` as the directory path(s) and `pattern=character(0)` as the pattern for discovering Solexa intensity files. See `readIntensities,character-method` for additional parameters.

readPrb

  `signature(dirPath = "SolexaPath", pattern=character(0), run, ...)`:

  Use `baseCallPath(dirPath)[run]` as the directory path(s) and `pattern=character(0)` as the pattern for discovering Solexa ‘prb’ files, returning a `SFastqQuality` object containing the maximum qualities found for each base of each cycle.

  The `...` argument may include the named argument `as`. This influences the return value, as explained on the `readPrb,character-method` page.

readFasta

  `signature(dirPath, pattern = character(0), ..., nrec=-1L, skip=0L)`:

  Use `analysisPath(dirPath)[run]` as the directory path(s) for discovering fasta-formatted files, returning a `ShortRead` object. The default method reads all files into a single object.

readFastq

  `signature(dirPath = "SolexaPath", pattern = ".*_sequence.txt", run, ..., qualityType="SFastqQuality")`:

  Use `analysisPath(dirPath)[run]` as the directory path(s) and `pattern=".*_sequence.txt"` as the pattern for discovering fastq-formatted files, returning a `ShortReadQ` object. The default method reads all sequence files into a single object.

readBaseQuality

  `signature(dirPath = "SolexaPath", seqPattern = ".*_seq.txt", prbPattern = "s_[1-8]_prb.txt", run, ...)`:

  Use `baseCallPath(dirPath)[run]` as the directory path(s) and `seqPattern=".*_seq.txt"` as the pattern for discovering base calls and `prbPattern=".*_prb.txt"` as the pattern for discovering quality scores. Note that the default method reads all base call and quality score files into a single object; often one will want to specify a pattern for each lane.

readQseq

  `signature(directory="SolexaPath", pattern=".*_qseq.txt.*", run, ...., filtered=FALSE)`:

  Use `analysisPath(dirPath)[run]` as the directory path and `pattern=".*_qseq.txt.*"` as the pattern for discovering read and quality scores in Solexa 'qseq' files. Data from all files are read into a single object; often one will want to specify a pattern for each lane. Details are as for `readQseq,character-method`.

readAligned

  `signature(dirPath = "SolexaPath", pattern = ".*_export.txt.*", run, ..., filter=srFilter())`:

  Use `analysisPath(dirPath)[run]` as the directory path and `pattern=".*_export.txt"` as the pattern for discovering Eland-aligned reads in the Solexa 'export' file format. Note that the default method reads all aligned read files into a single object; often one will want to specify a pattern for each lane. Use an object of `SRFilter` to select specific chromosomes, strands, etc.

qa

  `signature(dirPath="SolexaPath", pattern="character(0)", run, ...)`:

  Use `analysisPath(dirPath)[run]` as the directory path(s) and `pattern=".*_export.txt"` as the pattern for discovering Solexa `export`-formatted fileds, returning a `SolexaExportQA` object summarizing quality assessment. If `Rmpi` or `parallel` has been initiated, quality assessment calculations are distributed across available nodes or cores (one node per export file.)

report

  `signature(x, ..., dest=tempfile(), type="pdf")`: Use `qa(x, ...)` to generate quality assessment measures, and use these to generate a quality assessment report at location `dest` of type `type` (e.g., ‘pdf’).

SolexaSet

  `signature(path = "SolexaPath")`: create a `SolexaSet` object based on `path`.

Additional methods include:

show

  `signature(object = "SolexaPath")`: briefly summarize the file paths of `object`. The `experimentPath` is given in full; the remaining paths are identified by their leading characters.

detail

  `signature(x = "SolexaPath")`: summarize file paths of `x`. All file paths are presented in full.

### Author(s)

Martin Morgan

### Examples

    showClass("SolexaPath")
    showMethods(class="SolexaPath", where=getNamespace("ShortRead"))
    sf <- system.file("extdata", package="ShortRead")
    sp <- SolexaPath(sf)
    sp
    readFastq(sp, pattern="s_1_sequence.txt")
    ## Not run:
    nfiles <- length(list.files(analysisPath(sp), "s_[1-8]_export.txt"))
    library(Rmpi)
    mpi.spawn.Rslaves(nslaves=nfiles)
    report(qa(sp))

    ## End(Not run)
    ## Not run:
    nfiles <- length(list.files(analysisPath(sp), "s_[1-8]_export.txt"))
    report(qa(sp))

    ## End(Not run)

[Package ShortRead version 1.38.0 Index]