getVariable: Accessors for variables in GenotypeData and IntensityData...

In smgogarten/GWASTools: Tools for Genome Wide Association Studies

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

smgogarten/GWASTools documentation built on May 18, 2024, 1:19 a.m.