Affymetrix File Parsing SDK

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Documentation for package `affxparser' version 1.4.1

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affxparser-package Package affxparser
affxparser Package affxparser
affxparserInfo Overview of the Affxparser package.
applyCdfGroups Applies a function over the groups in a CDF structure
cdfAddBaseMmCounts Adds the number of allele A and allele B mismatching nucleotides of the probes in a CDF structure
cdfAddProbeOffsets Adds probe offsets to the groups in a CDF structure
cdfGetFields Gets a subset of groups fields in a CDF structure
cdfGtypeCelToPQ Function to immitate Affymetrix' gtype_cel_to_pq software
cdfMergeStrands Function to join CDF groups with the same names
cdfMergeToQuartets Function to re-arrange CDF groups values in quartets
cellindexmaps Cell index maps for reading and writing
cellxy Cell coordinates and cell indices
findCdf Search for CDF files in multiple directories
findFiles Finds one or several files in multiple directories
invertMap Inverts a read or a write map
read.affybatch2 Read CEL files into an Affybatch
readCdf Parsing a CDF file using Affymetrix Fusion SDK
readCdfCellIndices Reads cell indices of units (probesets) in an Affymetrix CDF file
readCdfGroupNames Reads group names of a set units (probesets) in an Affymetrix CDF file
readCdfHeader Reads the header associated with an Affymetrix CDF file
readCdfIsPm Checks if cells in a CDF file are perfect-match probes or not
readCdfNbrOfCellsPerUnitGroup Gets the number of cells (probes) that each group of each unit in a CDF file
readCdfUnitNames Reads unit (probeset) names from an Affymetrix CDF file
readCdfUnits Reads units (probesets) from an Affymetrix CDF file
readCdfUnitsWriteMap Generates an Affymetrix cell-index write map from a 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