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.
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.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.
basePathexperimentPath, above.dataPathscanPathimageAnalysisPathbaseCallPathanalysisPath".Solexa", directly.
Class ".ShortReadBase", by class ".Solexa", distance 2.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.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. 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.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.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 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.)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.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(x = "SolexaPath"): summarize
file paths of x. All file paths are presented in
full.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)
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