| 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"),
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, ...):
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.
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(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)