getVariable {GWASTools} | R Documentation

## Accessors for variables in GenotypeData and IntensityData classes and their component classes

### Description

These generic functions provide access to variables associated with GWAS data cleaning.

### Usage

      getScanAnnotation(object, ...)
      getScanVariable(object, varname, ...)
      getScanVariableNames(object, ...)
      getScanID(object, ...)
      getSex(object, ...)
      getSnpAnnotation(object, ...)
      getSnpVariable(object, varname, ...)
      getSnpVariableNames(object, ...)
      getSnpID(object, ...)
      getChromosome(object, ...)
      getPosition(object, ...)
      getAlleleA(object, ...)
      getAlleleB(object, ...)

      getVariable(object, varname, ...)
      getVariableNames(object, ...)
      getGenotype(object, ...)
      getGenotypeSelection(object, ...)
      getQuality(object, ...)
      getX(object, ...)
      getY(object, ...)
      getBAlleleFreq(object, ...)
      getLogRRatio(object, ...)
      getDimension(object, varname, ...)
      getAttribute(object, attname, varname, ...)
      getNodeDescription(object, varname, ...)

      getAnnotation(object, ...)
      getMetadata(object, ...)
      getQuery(object, statement, ...)

      hasScanAnnotation(object)
      hasScanVariable(object, varname)
      hasSex(object)
      hasSnpAnnotation(object)
      hasSnpVariable(object, varname)
      hasVariable(object, varname)
      hasQuality(object)
      hasX(object)
      hasY(object)
      hasBAlleleFreq(object)
      hasLogRRatio(object)

      nsnp(object)
      nscan(object)

      autosomeCode(object)
      XchromCode(object)
      XYchromCode(object)
      YchromCode(object)
      MchromCode(object)

      writeAnnotation(object, value, ...)
      writeMetadata(object, value, ...)

### Arguments

`object` | Object, possibly derived from or containing `NcdfReader-class`, `GdsReader-class`, `ScanAnnotationDataFrame-class`, `SnpAnnotationDataFrame-class`, `ScanAnnotationSQLite-class`, or `SnpAnnotationSQLite-class`.
`varname` | Name of the variable (single character string, or a character vector for multiple variables).
`attname` | Name of an attribute.
`statement` | SQL statement to query `ScanAnnotationSQLite-class` or `SnpAnnotationSQLite-class` objects.
`value` | data.frame with annotation or metadata to write to `ScanAnnotationSQLite-class` or `SnpAnnotationSQLite-class` objects.
`...` | Additional arguments.

### Value

`get` methods return vectors or matrices of the requested variables (with the exception of `getQuery`, which returns a data frame).

`has` methods return TRUE if the requested variable is present in `object`.

`nsnp` and `nscan` return the number of SNPs and scans in the object, repectively.

`autosomeCode`, `XchromCode`, `XYchromCode`, `YchromCode`, and `MchromCode` return the integer chromosome codes associated with autosomal, X, pseudoautosomal, Y, and mitochondrial SNPs.

### Author(s)

Stephanie Gogarten

### See Also

`ScanAnnotationDataFrame-class`, `SnpAnnotationDataFrame-class`, `ScanAnnotationSQLite-class`, `SnpAnnotationSQLite-class`, `NcdfReader-class`, `NcdfGenotypeReader-class`, `NcdfIntensityReader-class`, `GdsReader-class`, `GdsGenotypeReader-class`, `GdsIntensityReader-class`, `GenotypeData-class`, `IntensityData-class`

[Package GWASTools version 1.40.0 Index]