ScanAnnotationSQLite {GWASTools} | R Documentation

## Class ScanAnotationSQLite

### Description

The ScanAnnotationSQLite class stores annotation data associated with scans, as well as metadata describing each column, in an SQLite database.

### Constructor

  `ScanAnnotationSQLite(dbpath)`:

  `dbpath` is the path to a SQLite database with tables "Annotation" and "Metadata." "Annotation" 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" must contain at least the following columns:

  - "varname": name of variable in annotation

  - "description": description of column in annotation

  If the database does not yet exist, a database is created with tables "Annotation" and "Metadata."

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

### Accessors

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

  `open(object)`: Opens a connection to the database.

  `close(object)`: Closes the database connection.

  `nscan(object)`: The number of scans in the database.

  `getScanID(object, index, condition)`: A unique vector of scan IDs. The optional `index` is a logical or integer vector specifying elements to extract. The optional `condition` is a character string with an SQL clause used to select data (e.g., "LIMIT 10", "WHERE sex='M'").

  `getSex(object, index, condition)`: A character vector of sex, with values 'M' or 'F'. The optional `index` is a logical or integer vector specifying elements to extract. The optional `condition` is a character string with an SQL clause used to select data.

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

  `getVariable(object, varname, index, condition)`: A vector of the column `varname`. The optional `index` is a logical or integer vector specifying elements to extract. The optional `condition` is a character string with an SQL clause used to select data (e.g., "LIMIT 10", "WHERE sex='M'"). 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.

  `getQuery(object, statement)`: Returns result of the SQL query `statement`.

  `writeAnnotation(object, value, append=FALSE, overwrite=TRUE)`: Writes `value` to the scan annotation table. `value` must be a data.frame containing a column "scanID".

  `writeMetadata(object, value, append=FALSE, overwrite=TRUE)`: Writes `value` to the metadata table. `value` should be a data.frame containing columns "varname" and "description".

### Author(s)

Stephanie Gogarten

### See Also

`SnpAnnotationSQLite`, `ScanAnnotationDataFrame`, `GenotypeData`, `IntensityData`

### Examples

    library(GWASdata)
    dbpath <- tempfile()
    scanAnnot <- ScanAnnotationSQLite(dbpath)

    data(illumina_scan_annot)
    writeAnnotation(scanAnnot, illumina_scan_annot)

    # list columns
    vars <- getVariableNames(scanAnnot)

    # add metadata
    metadf <- data.frame(varname=vars, description=rep(NA, length(vars)),
      row.names=vars, stringsAsFactors=FALSE)
    metadf["scanID", "description"] <- "unique id"
    writeMetadata(scanAnnot, metadf)

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

    # display data
    head(getAnnotation(scanAnnot))
    getMetadata(scanAnnot)

    close(scanAnnot)
    file.remove(dbpath)

[Package GWASTools version 1.28.0 Index]