ScanAnnotationDataFrame {GWASTools} | R Documentation

## Class ScanAnotationDataFrame

### Description

The ScanAnnotationDataFrame class stores annotation data associated with subjects in a genotyping study, where there may be multiple scans per subject, as well as metadata describing each column. It extends the `AnnotatedDataFrame` class.

### Extends

`AnnotatedDataFrame`

### Constructor

  `ScanAnnotationDataFrame(data, metadata)`:

  `data` must be a data.frame containing the scan annotation. It must contain at least the following column:

  - "scanID": vector containing unique scan ids.

  If a column representing sex is present, it must have the following format:

  - "sex": character vector with values 'M' or 'F'.

  `metadata` is an optional data.frame containing a description for each column in `data`. It should contain a column "labelDescription", with `row.names(metadata) == names(data)`.

  The `ScanAnnotationDataFrame` constructor creates and returns a ScanAnnotationDataFrame instance.

### Accessors

In the code snippets below, `object` is a ScanAnnotationDataFrame object.

  `getScanID(object, index)`: A unique vector of scan IDs. The optional `index` is a logical or integer vector specifying elements to extract.

  `getSex(object, index)`: A character vector of sex, with values 'M' or 'F'. The optional `index` is a logical or integer vector specifying elements to extract.

  `hasSex(object)`: Returns `TRUE` if the column 'sex' is present in `object`.

  `getVariable(object, varname, index)`: A vector of the column `varname`. The optional `index` is a logical or integer vector specifying elements to extract. If `varname` is itself a vector, returns a data.frame. Returns `NULL` if `varname` is not found in `object`.

  `hasVariable(object, varname)`: Returns `TRUE` if `varname` is a column in `object`, `FALSE` if not.

  `getVariableNames(object)`: Returns a character vector with the names of all columns in `object`.

  `getAnnotation(object)`: Returns all annotation variables as a data frame.

  `getMetadata(object)`: Returns metadata describing the annotation variables as a data frame.

Inherited methods from `AnnotatedDataFrame`:

  `varLabels(object)`: Returns a character vector with the names of all columns in `object`.

  `pData(object)`: Returns all annotation variables as a data frame, or sets the annotation variables with `pData(object) <- df`.

  `varMetadata(object)`: Returns metadata describing the annotation variables as a data frame, or sets the metadata with `varMetadata(object) <- df`.

  The operators `$` and `[` work just as they do in standard data frames, for both retrieval and assignment.

### Author(s)

Stephanie Gogarten

### See Also

`AnnotatedDataFrame`, `SnpAnnotationDataFrame`, `GenotypeData`, `IntensityData`

### Examples

    library(GWASdata)
    data(illumina_scan_annot)
    scanAnnot <- ScanAnnotationDataFrame(illumina_scan_annot)

    scanID <- getScanID(scanAnnot)
    sex <- getSex(scanAnnot)
    if (hasVariable(scanAnnot, "plate")) plate <- getVariable(scanAnnot, "plate")
    subjectID <- getVariable(scanAnnot, "subjectID", index=(sex == "M"))

    # list columns
    varLabels(scanAnnot)

    # add metadata
    meta <- varMetadata(scanAnnot)
    meta["scanID", "labelDescription"] <- "unique scan ID"
    varMetadata(scanAnnot) <- meta

    # display data
    head(pData(scanAnnot))

    # standard operators
    scanID <- scanAnnot$scanID
    sex <- scanAnnot[["sex"]]
    subset <- scanAnnot[1:10, 1:5]
    scanAnnot$newVar <- rep(1, nrow(scanAnnot))

    # replace data
    df <- pData(scanAnnot)
    pData(scanAnnot) <- df

[Package GWASTools version 1.28.0 Index]