(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).

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.

Author(s)

Martin Morgan

Examples

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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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