SolexaPath-class: (Legacy) "SolexaPath" class representing a standard output...

In Bioconductor/ShortRead: FASTQ input and manipulation

(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)

Bioconductor/ShortRead documentation built on Nov. 2, 2024, 4:38 p.m.