SolexaSet-class: (Legacy) "SolexaSet" coordinating Solexa output locations with sample annotations

Description

This class coordinates the file hierarchy produced by the Solexa `pipeline' with annotation data contained in an AnnotatedDataFrame (defined in the Biobase package).

Arguments

Objects from the Class

Objects can be created from the constructor: SolexaSet(path, ...).

path: A character(1) vector giving the fully-qualified path to the root of the directory hierarchy associated with each Solexa flow cell, or an object of class SolexaPath (see SolexaPath for this method).
...: Additional arguments, especially laneDescription, an AnnotatedDataFrame describing the content of each of the 8 lanes in the Solexa flow cell.

Slots

SolexaSet has the following slots:

solexaPath:: Object of class "SolexaPath".
laneDescription:: Object of class "AnnotatedDataFrame", containing information about the samples in each lane of the flow cell.

Extends

Class ".Solexa", directly. Class ".ShortReadBase", by class ".Solexa", distance 2.

Methods

solexaPath: signature(object = "SolexaSet"): Return the directory paths present when this object was created as a SolexaPath.
laneNames: signature(object = "SolexaSet"): Return the names of each lane in the flow cell, currently names are simply 1:8.
show: signature(object = "SolexaSet"): Briefly summarize the experiment path and lane description of the Solexa set.
detail: signature(x = "SolexaSet"): Provide additional detail on the Solexa set, including the content of solexaPath and the pData and varMetadata of laneDescription.

Methods transforming SolexaSet objects include:

readAligned: signature(dirPath = "SolexaSet", pattern = ".*_export.txt", run, ..., filter=srFilter()): Use analysisPath(solexaPath(dirPath))[run] as the directory path(s) 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.

Examples

Run this code

showClass("SolexaSet")
showMethods(class="SolexaSet", where=getNamespace("ShortRead"))
## construct a SolexaSet
sf <- system.file("extdata", package="ShortRead")
df <- data.frame(Sample=c("Sample 1", "Sample 2", "Sample 3", "Sample
                          4", "Center-wide control", "Sample 6", "Sample
                          7", "Sample 8"),
                 Genome=c(rep("hg18", 4), "phi_plus_SNPs.txt",
                          rep("hg18", 3)))
dfMeta <- data.frame(labelDescription=c("Type of sample",
                                        "Alignment genome"))
adf <- new("AnnotatedDataFrame", data=df, varMetadata=dfMeta)
SolexaSet(sf, adf)

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