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.
experimentPath
dataPath
scanPath
imageAnalysisPath
baseCallPath
analysisPath
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)