SolexaSet-class {ShortRead} | R Documentation

## (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

    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)

[Package ShortRead version 1.38.0 Index]