| SolexaPath-class {ShortRead} | R Documentation |
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 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)
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 argumentTRUE results in warnings if paths do not exist.All paths must be fully-specified.
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.
experimentPathdataPathscanPathimageAnalysisPathbaseCallPathanalysisPath
Class ".Solexa", directly.
Class ".ShortReadBase", by class ".Solexa", distance 2.
Transforming methods include:
signature(dirPath = "SolexaPath", pattern=character(0), run,
..., intExtension = "_int.txt", nseExtension = "_nse.txt",
withVariability = TRUE, verbose = FALSE):
Use imageAnalysisPath(sp)[run] as the directory path(s) and
pattern=character(0) as the pattern for discovering Soelxa
intExtension and nseExtension files, returning a
SolexaIntensity object containing
intensities, (optionally) standard errors, and read (lane, tile,
x, y coordinates of cluster) information.
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, retuning 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.
signature(dirPath = "SolexaPath", pattern = ".*_sequence.txt", run, ...):
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. Note that the default
method reads all sequence files into a single object; often
one will want to specify a pattern for each lane.
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.
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.
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.
signature(dirPath="SolexaPath", pattern="character(0)", run, ...):
Use analysisPath(dirPath)[run] as the directorpy path(s) and
pattern=".*_export.txt" as the pattern for discovering solexa
export-formatted fileds, returning a
SolexaExportQA object summarizing quality
assessment. If Rmpi has been initiated, quality assessment
calculations are distributed across available nodes (one node per
export file.)
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’).
signature(path = "SolexaPath"): create a
SolexaSet object based on path.
Additional methods include:
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.signature(object = "SolexaPath"): summarize
file paths of object. All file paths are presented in
full.Martin Morgan
showClass("SolexaPath")
showMethods(class="SolexaPath")
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)