Entry: 1. Dictionary
Aliases: 1. Dictionary
Keywords: documentation
Description: 1. Dictionary
URL: ../../../library/affxparser/html/1._Dictionary.html

Entry: 2. Cell coordinates and cell indices
Aliases: 2. Cell coordinates and cell indices
Keywords: documentation
Description: 2. Cell coordinates and cell indices
URL: ../../../library/affxparser/html/2._Cell_coordinates_and_cell_indices.html

Entry: 9. Advanced - Cell-index maps for reading and writing
Aliases: 9. Advanced - Cell-index maps for reading and writing
Keywords: documentation internal
Description: 9. Advanced - Cell-index maps for reading and writing
URL: ../../../library/affxparser/html/9._Advanced_-_Cell-index_maps_for_reading_and_writing.html

Entry: affxparser-package
Aliases: affxparser-package affxparser
Keywords: package
Description: Package affxparser
URL: ../../../library/affxparser/html/affxparser-package.html

Entry: applyCdfGroups
Aliases: applyCdfGroups applyCdfBlocks
Keywords: programming
Description: Applies a function over the groups in a CDF structure
URL: ../../../library/affxparser/html/applyCdfGroups.html

Entry: cdfAddBaseMmCounts
Aliases: cdfAddBaseMmCounts
Keywords: programming internal
Description: Adds the number of allele A and allele B mismatching nucleotides of the probes in a CDF structure
URL: ../../../library/affxparser/html/cdfAddBaseMmCounts.html

Entry: cdfAddPlasqTypes
Aliases: cdfAddPlasqTypes
Keywords: programming internal
Description: Adds the PLASQ types for the probes in a CDF structure
URL: ../../../library/affxparser/html/cdfAddPlasqTypes.html

Entry: cdfAddProbeOffsets
Aliases: cdfAddProbeOffsets
Keywords: programming internal
Description: Adds probe offsets to the groups in a CDF structure
URL: ../../../library/affxparser/html/cdfAddProbeOffsets.html

Entry: cdfGetFields
Aliases: cdfGetFields
Keywords: programming internal
Description: Gets a subset of groups fields in a CDF structure
URL: ../../../library/affxparser/html/cdfGetFields.html

Entry: cdfGetGroups
Aliases: cdfGetGroups
Keywords: programming internal
Description: Gets a subset of groups in a CDF structure
URL: ../../../library/affxparser/html/cdfGetGroups.html

Entry: cdfGtypeCelToPQ
Aliases: cdfGtypeCelToPQ
Keywords: programming internal
Description: Function to immitate Affymetrix' gtype\_cel\_to\_pq software
URL: ../../../library/affxparser/html/cdfGtypeCelToPQ.html

Entry: cdfHeaderToCelHeader
Aliases: cdfHeaderToCelHeader
Keywords: programming internal
Description: Creates a valid CEL header from a CDF header
URL: ../../../library/affxparser/html/cdfHeaderToCelHeader.html

Entry: cdfMergeAlleles
Aliases: cdfMergeAlleles
Keywords: programming internal
Description: Function to join CDF allele A and allele B groups strand by strand
URL: ../../../library/affxparser/html/cdfMergeAlleles.html

Entry: cdfMergeStrands
Aliases: cdfMergeStrands
Keywords: programming internal
Description: Function to join CDF groups with the same names
URL: ../../../library/affxparser/html/cdfMergeStrands.html

Entry: cdfMergeToQuartets
Aliases: cdfMergeToQuartets
Keywords: programming internal
Description: Function to re-arrange CDF groups values in quartets
URL: ../../../library/affxparser/html/cdfMergeToQuartets.html

Entry: cdfOrderBy
Aliases: cdfOrderBy
Keywords: programming internal
Description: Orders the fields according to the value of another field in the same CDF group
URL: ../../../library/affxparser/html/cdfOrderBy.html

Entry: cdfOrderColumnsBy
Aliases: cdfOrderColumnsBy
Keywords: programming internal
Description: Orders the columns of fields according to the values in a certain row of another field in the same CDF group
URL: ../../../library/affxparser/html/cdfOrderColumnsBy.html

Entry: compareCdfs
Aliases: compareCdfs
Keywords: file IO
Description: Compares the contents of two CDF files
URL: ../../../library/affxparser/html/compareCdfs.html

Entry: compareCels
Aliases: compareCels
Keywords: file IO
Description: Compares the contents of two CEL files
URL: ../../../library/affxparser/html/compareCels.html

Entry: convertCdf
Aliases: convertCdf
Keywords: file IO
Description: Converts a CDF into the same CDF but with another format
URL: ../../../library/affxparser/html/convertCdf.html

Entry: convertCel
Aliases: convertCel
Keywords: file IO
Description: Converts a CEL into the same CEL but with another format
URL: ../../../library/affxparser/html/convertCel.html

Entry: copyCel
Aliases: copyCel
Keywords: programming file IO internal
Description: Copies a CEL file
URL: ../../../library/affxparser/html/copyCel.html

Entry: createCel
Aliases: createCel
Keywords: file IO
Description: Creates an empty CEL file
URL: ../../../library/affxparser/html/createCel.html

Entry: findCdf
Aliases: findCdf
Keywords: file IO
Description: Search for CDF files in multiple directories
URL: ../../../library/affxparser/html/findCdf.html

Entry: findFiles
Aliases: findFiles
Keywords: file IO internal
Description: Finds one or several files in multiple directories
URL: ../../../library/affxparser/html/findFiles.html

Entry: invertMap
Aliases: invertMap
Keywords: file IO internal
Description: Inverts a read or a write map
URL: ../../../library/affxparser/html/invertMap.html

Entry: isCelFile
Aliases: isCelFile
Keywords: programming file IO internal
Description: Checks if a file is a CEL file or not
URL: ../../../library/affxparser/html/isCelFile.html

Entry: readBpmap
Aliases: readBpmap readBpmapHeader readBpmapSeqinfo
Keywords: file IO
Description: Parses a Bpmap file
URL: ../../../library/affxparser/html/readBpmap.html

Entry: readCcg
Aliases: readCcg
Keywords: file IO
Description: Reads an Affymetrix Command Console Generic (CCG) Data file
URL: ../../../library/affxparser/html/readCcg.html

Entry: readCcgHeader
Aliases: readCcgHeader
Keywords: file IO
Description: Reads an the header of an Affymetrix Command Console Generic (CCG) file
URL: ../../../library/affxparser/html/readCcgHeader.html

Entry: readCdf
Aliases: readCdf
Keywords: file IO internal
Description: Parsing a CDF file using Affymetrix Fusion SDK
URL: ../../../library/affxparser/html/readCdf.html

Entry: readCdfCellIndices
Aliases: readCdfCellIndices
Keywords: file IO
Description: Reads cell indices of units (probesets) in an Affymetrix CDF file
URL: ../../../library/affxparser/html/readCdfCellIndices.html

Entry: readCdfDataFrame
Aliases: readCdfDataFrame
Keywords: file IO internal
Description: Reads units (probesets) from an Affymetrix CDF file
URL: ../../../library/affxparser/html/readCdfDataFrame.html

Entry: readCdfGroupNames
Aliases: readCdfGroupNames
Keywords: file IO
Description: Reads group names for a set of units (probesets) in an Affymetrix CDF file
URL: ../../../library/affxparser/html/readCdfGroupNames.html

Entry: readCdfHeader
Aliases: readCdfHeader
Keywords: file IO
Description: Reads the header associated with an Affymetrix CDF file
URL: ../../../library/affxparser/html/readCdfHeader.html

Entry: readCdfIsPm
Aliases: readCdfIsPm
Keywords: file IO internal
Description: Checks if cells in a CDF file are perfect-match probes or not
URL: ../../../library/affxparser/html/readCdfIsPm.html

Entry: readCdfNbrOfCellsPerUnitGroup
Aliases: readCdfNbrOfCellsPerUnitGroup
Keywords: file IO internal
Description: Gets the number of cells (probes) that each group of each unit in a CDF file
URL: ../../../library/affxparser/html/readCdfNbrOfCellsPerUnitGroup.html

Entry: readCdfQc
Aliases: readCdfQc
Keywords: file IO internal
Description: Reads the QC units of CDF file
URL: ../../../library/affxparser/html/readCdfQc.html

Entry: readCdfUnitNames
Aliases: readCdfUnitNames
Keywords: file IO
Description: Reads unit (probeset) names from an Affymetrix CDF file
URL: ../../../library/affxparser/html/readCdfUnitNames.html

Entry: readCdfUnits
Aliases: readCdfUnits
Keywords: file IO
Description: Reads units (probesets) from an Affymetrix CDF file
URL: ../../../library/affxparser/html/readCdfUnits.html

Entry: readCdfUnitsWriteMap
Aliases: readCdfUnitsWriteMap
Keywords: file IO internal
Description: Generates an Affymetrix cell-index write map from a CDF file
URL: ../../../library/affxparser/html/readCdfUnitsWriteMap.html

Entry: readCel
Aliases: readCel
Keywords: file IO
Description: Reads an Affymetrix CEL file
URL: ../../../library/affxparser/html/readCel.html

Entry: readCelHeader
Aliases: readCelHeader
Keywords: file IO
Description: Parsing the header of an Affymetrix CEL file
URL: ../../../library/affxparser/html/readCelHeader.html

Entry: readCelIntensities
Aliases: readCelIntensities
Keywords: file IO
Description: Reads the intensities contained in several Affymetrix CEL files
URL: ../../../library/affxparser/html/readCelIntensities.html

Entry: readCelRectangle
Aliases: readCelRectangle
Keywords: file IO
Description: Reads a spatial subset of probe-level data from Affymetrix CEL files
URL: ../../../library/affxparser/html/readCelRectangle.html

Entry: readCelUnits
Aliases: readCelUnits
Keywords: file IO
Description: Reads probe-level data ordered as units (probesets) from one or several Affymetrix CEL files
URL: ../../../library/affxparser/html/readCelUnits.html

Entry: readChp
Aliases: readChp
Keywords: file IO
Description: A function to read Affymetrix CHP files
URL: ../../../library/affxparser/html/readChp.html

Entry: readClf
Aliases: readClf
Keywords: file IO
Description: Parsing a CLF file using Affymetrix Fusion SDK
URL: ../../../library/affxparser/html/readClf.html

Entry: readClfEnv
Aliases: readClfEnv
Keywords: file IO
Description: Parsing a CLF file using Affymetrix Fusion SDK
URL: ../../../library/affxparser/html/readClfEnv.html

Entry: readClfHeader
Aliases: readClfHeader
Keywords: IO
Description: Read the header of a CLF file.
URL: ../../../library/affxparser/html/readClfHeader.html

Entry: readPgf
Aliases: readPgf
Keywords: file IO
Description: Parsing a PGF file using Affymetrix Fusion SDK
URL: ../../../library/affxparser/html/readPgf.html

Entry: readPgfEnv
Aliases: readPgfEnv
Keywords: file IO
Description: Parsing a PGF file using Affymetrix Fusion SDK
URL: ../../../library/affxparser/html/readPgfEnv.html

Entry: readPgfHeader
Aliases: readPgfHeader
Keywords: file IO
Description: Read the header of a PGF file into a list.
URL: ../../../library/affxparser/html/readPgfHeader.html

Entry: updateCel
Aliases: updateCel
Keywords: file IO
Description: Updates a CEL file
URL: ../../../library/affxparser/html/updateCel.html

Entry: updateCelUnits
Aliases: updateCelUnits
Keywords: file IO
Description: Updates a CEL file unit by unit
URL: ../../../library/affxparser/html/updateCelUnits.html

Entry: writeCdf
Aliases: writeCdf
Keywords: file IO internal
Description: Creates a binary CDF file
URL: ../../../library/affxparser/html/writeCdf.html

Entry: writeCdfHeader
Aliases: writeCdfHeader
Keywords: file IO internal
Description: Writes a CDF header
URL: ../../../library/affxparser/html/writeCdfHeader.html

Entry: writeCdfQcUnits
Aliases: writeCdfQcUnits
Keywords: file IO internal
Description: Writes CDF QC units
URL: ../../../library/affxparser/html/writeCdfQcUnits.html

Entry: writeCdfUnits
Aliases: writeCdfUnits
Keywords: file IO internal
Description: Writes CDF units
URL: ../../../library/affxparser/html/writeCdfUnits.html

Entry: writeCelHeader
Aliases: writeCelHeader
Keywords: file IO internal
Description: Writes a CEL header to a connection
URL: ../../../library/affxparser/html/writeCelHeader.html

Entry: writeTpmap
Aliases: writeTpmap tpmap2bpmap
Keywords: file IO
Description: Writes BPMAP and TPMAP files.
URL: ../../../library/affxparser/html/writeTpmap.html
