affxparser v1.44.0

Affymetrix File Parsing SDK

Package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). It provides methods for fast and memory efficient parsing of Affymetrix files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files are supported. Currently, there are methods for reading chip definition file (CDF) and a cell intensity file (CEL). These files can be read either in full or in part. For example, probe signals from a few probesets can be extracted very quickly from a set of CEL files into a convenient list structure.

Readme

affxparser: Affymetrix File Parsing SDK

Installation

R package affxparser is available on Bioconductor and can be installed in R as:

source('http://bioconductor.org/biocLite.R')
biocLite('affxparser')

Software status

Resource: Bioconductor Travis CI Appveyor
Platforms: Multiple Linux Windows
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Functions in affxparser

Name Description
cdfGtypeCelToPQ Function to immitate Affymetrix' gtype\_cel\_to\_pq software
findFiles Finds one or several files in multiple directories
compareCels Compares the contents of two CEL files
readCdfUnitNames Reads unit (probeset) names from an Affymetrix CDF file
readCcgHeader Reads an the header of an Affymetrix Command Console Generic (CCG) file
readBpmap Parses a Bpmap file
createCel Creates an empty CEL file
convertCdf Converts a CDF into the same CDF but with another format
readCdfCellIndices Reads (one-based) cell indices of units (probesets) in an Affymetrix CDF file
readCel Reads an Affymetrix CEL file
readCdfHeader Reads the header associated with an Affymetrix CDF file
readClfHeader Read the header of a CLF file.
cdfSetDimension Sets the dimension of an object
readCelIntensities Reads the intensities contained in several Affymetrix CEL files
readPgfEnv Parsing a PGF file using Affymetrix Fusion SDK
readPgfHeader Read the header of a PGF file into a list.
cdfMergeStrands Function to join CDF groups with the same names
cdfMergeToQuartets Function to re-arrange CDF groups values in quartets
readPgf Parsing a PGF file using Affymetrix Fusion SDK
updateCelUnits Updates a CEL file unit by unit
parseDatHeaderString Parses a DAT header string
readCdfUnits Reads units (probesets) from an Affymetrix CDF file
readCdfIsPm Checks if cells in a CDF file are perfect-match probes or not
readCdfUnitsWriteMap Generates an Affymetrix cell-index write map from a CDF file
writeCelHeader Writes a CEL header to a connection
readCdf Parsing a CDF file using Affymetrix Fusion SDK
readCdfNbrOfCellsPerUnitGroup Gets the number of cells (probes) that each group of each unit in a CDF file
readCelRectangle Reads a spatial subset of probe-level data from Affymetrix CEL files
writeCdfQcUnits Writes CDF QC units
readClfEnv Parsing a CLF file using Affymetrix Fusion SDK
writeCdf Creates a binary CDF file
affxparser-package Package affxparser
readCcg Reads an Affymetrix Command Console Generic (CCG) Data file
readChp A function to read Affymetrix CHP files
writeCdfHeader Writes a CDF header
2. Cell coordinates and cell indices 2. Cell coordinates and cell indices
9. Advanced - Cell-index maps for reading and writing 9. Advanced - Cell-index maps for reading and writing
cdfHeaderToCelHeader Creates a valid CEL header from a CDF header
convertCel Converts a CEL into the same CEL but with another format
isCelFile Checks if a file is a CEL file or not
readCelHeader Parsing the header of an Affymetrix CEL file
writeCdfUnits Writes CDF units
applyCdfGroupFields Applies a function to a list of fields of each group in a CDF structure
readCelUnits Reads probe-level data ordered as units (probesets) from one or several Affymetrix CEL files
readClf Parsing a CLF file using Affymetrix Fusion SDK
cdfOrderColumnsBy Orders the columns of fields according to the values in a certain row of another field in the same CDF group
writeTpmap Writes BPMAP and TPMAP files.
cdfGetFields Gets a subset of groups fields in a CDF structure
1. Dictionary 1. Dictionary
cdfOrderBy Orders the fields according to the value of another field in the same CDF group
compareCdfs Compares the contents of two CDF files
invertMap Inverts a read or a write map
readCdfDataFrame Reads units (probesets) from an Affymetrix CDF file
copyCel Copies a CEL file
cdfAddBaseMmCounts Adds the number of allele A and allele B mismatching nucleotides of the probes in a CDF structure
cdfGetGroups Gets a subset of groups in a CDF structure
findCdf Search for CDF files in multiple directories
cdfAddProbeOffsets Adds probe offsets to the groups in a CDF structure
arrangeCelFilesByChipType Moves CEL files to subdirectories with names corresponding to the chip types
applyCdfGroups Applies a function over the groups in a CDF structure
cdfMergeAlleles Function to join CDF allele A and allele B groups strand by strand
readCdfQc Reads the QC units of CDF file
updateCel Updates a CEL file
cdfAddPlasqTypes Adds the PLASQ types for the probes in a CDF structure
readCdfGroupNames Reads group names for a set of units (probesets) in an Affymetrix CDF file
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Last year downloads

Details

Date 2016-04-04
Note Fusion SDK v1.1.2
License LGPL (>= 2)
LazyLoad yes
URL https://github.com/HenrikBengtsson/affxparser
BugReports https://github.com/HenrikBengtsson/affxparser/issues
biocViews Infrastructure, DataImport, Microarray, ProprietaryPlatforms, OneChannel

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