| AffymetrixCdfFile.fromFile {aroma.affymetrix} | Defines an AffymetrixCdfFile object from a CDF file |
| AffymetrixCdfFile.fromFile {aroma.affymetrix} | Defines an AffymetrixCdfFile object from a CDF file |
| AffymetrixCdfFile.getAlleleCellPairs {aroma.affymetrix} | Gets the cell indices of allele pairs |
| AffymetrixCdfFile.getAlleleProbePairs {aroma.affymetrix} | Gets the indices of probepairs with the same pair of SNP nucleotides |
| AffymetrixCdfFile.getAlleleProbePairs3 {aroma.affymetrix} | Gets the indices of probepairs with the same pair of SNP nucleotides |
| AffymetrixCdfFile.getCellIndices {aroma.affymetrix} | Gets the cell indices unit by unit |
| AffymetrixCdfFile.getCnNames {aroma.affymetrix} | Gets the names of the CN units |
| AffymetrixCdfFile.getGenomeInformation {aroma.affymetrix} | Gets genome information for this chip type |
| AffymetrixCdfFile.getHeader {aroma.affymetrix} | Gets the header of the CDF file |
| AffymetrixCdfFile.getSnpNames {aroma.affymetrix} | Gets the names of the SNP units |
| AffymetrixCdfFile.getUnitNames {aroma.affymetrix} | Gets the names of each unit |
| AffymetrixCdfFile.getUnitTypes {aroma.affymetrix} | Gets the types of a set of units |
| AffymetrixCdfFile.groupUnitsByDimension {aroma.affymetrix} | Groups units by dimensions |
| AffymetrixCdfFile.isPm {aroma.affymetrix} | Checks which cells (probes) are PMs and not |
| AffymetrixCdfFile.isResequenceChip {aroma.affymetrix} | Static method to check if a CDF is for a resequencing (CustomSeq) chip |
| AffymetrixCdfFile.isSnpChip {aroma.affymetrix} | Static method to check if a chip is a mapping (SNP) chip |
| AffymetrixCdfFile.nbrOfGroupsPerUnit {aroma.affymetrix} | Gets the number of groups in each unit |
| AffymetrixCdfFile.nbrOfSnps {aroma.affymetrix} | Gets the number of SNPs |
| AffymetrixCdfFile.readUnits {aroma.affymetrix} | Reads CDF data unit by unit |
| AffymetrixCdfFile.readUnitsByQuartets {aroma.affymetrix} | Gets the cell quartets for each base position |
