Affymetrix File Parsing SDK

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Documentation for package ‘affxparser’ version 1.52.0

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affxparser-package Package affxparser
1. Dictionary 1. Dictionary
2. Cell coordinates and cell indices 2. Cell coordinates and cell indices
affxparser Package affxparser
applyCdfBlocks Applies a function over the groups in a CDF structure
applyCdfGroupFields Applies a function to a list of fields of each group in a CDF structure
applyCdfGroups Applies a function over the groups in a CDF structure
compareCdfs Compares the contents of two CDF files
compareCels Compares the contents of two CEL files
convertCdf Converts a CDF into the same CDF but with another format
convertCel Converts a CEL into the same CEL but with another format
createCel Creates an empty CEL file
findCdf Search for CDF files in multiple directories
readBpmap Parses a Bpmap file
readBpmapHeader Parses a Bpmap file
readBpmapSeqinfo Parses a Bpmap file
readCcg Reads an Affymetrix Command Console Generic (CCG) Data file
readCcgHeader Reads an the header of an Affymetrix Command Console Generic (CCG) file
readCdfCellIndices Reads (one-based) cell indices of units (probesets) in an Affymetrix CDF file
readCdfGroupNames Reads group names for a set of units (probesets) in an Affymetrix CDF file
readCdfHeader Reads the header associated with an Affymetrix CDF file
readCdfUnitNames Reads unit (probeset) names from an Affymetrix CDF file
readCdfUnits Reads units (probesets) from an Affymetrix CDF file
readCel Reads an Affymetrix CEL file
readCelHeader Parsing the header of an Affymetrix CEL file
readCelIntensities Reads the intensities contained in several Affymetrix CEL files
readCelRectangle Reads a spatial subset of probe-level data from Affymetrix CEL files
readCelUnits Reads probe-level data ordered as units (probesets) from one or several Affymetrix CEL files
readChp A function to read Affymetrix CHP files
readClf Parsing a CLF file using Affymetrix Fusion SDK
readClfEnv Parsing a CLF file using Affymetrix Fusion SDK
readClfHeader Read the header of a CLF file.
readPgf Parsing a PGF file using Affymetrix Fusion SDK
readPgfEnv Parsing a PGF file using Affymetrix Fusion SDK
readPgfHeader Read the header of a PGF file into a list.
tpmap2bpmap Writes BPMAP and TPMAP files.
updateCel Updates a CEL file
updateCelUnits Updates a CEL file unit by unit
writeTpmap Writes BPMAP and TPMAP files.