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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
R CMD check	(release) (devel)
Test coverage

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Version

Version

1.44.0

License

LGPL (>= 2)

Issues

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Repository

https://github.com/HenrikBengtsson/affxparser

Maintainer

Kasper Daniel Hansen

Last Published

February 15th, 2017

Functions in affxparser (1.44.0)

cdfGtypeCelToPQ

Function to immitate Affymetrix' gtype\_cel\_to\_pq software

Finds one or several files in multiple directories

Compares the contents of two CEL files

readCdfUnitNames

Reads unit (probeset) names from an Affymetrix CDF file

Reads an the header of an Affymetrix Command Console Generic (CCG) file

Parses a Bpmap file

Creates an empty CEL file

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

Reads an Affymetrix CEL file

Reads the header associated with an Affymetrix CDF file

Read the header of a CLF file.

cdfSetDimension

Sets the dimension of an object

readCelIntensities

Reads the intensities contained in several Affymetrix CEL files

Parsing a PGF file using Affymetrix Fusion SDK

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

Parsing a PGF file using Affymetrix Fusion SDK

Updates a CEL file unit by unit

parseDatHeaderString

Parses a DAT header string

Reads units (probesets) from an Affymetrix CDF file

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

Writes a CEL header to a connection

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

Parsing a CLF file using Affymetrix Fusion SDK

Creates a binary CDF file

affxparser-package

Package affxparser

Reads an Affymetrix Command Console Generic (CCG) Data file

A function to read Affymetrix CHP files

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

Converts a CEL into the same CEL but with another format

Checks if a file is a CEL file or not

Parsing the header of an Affymetrix CEL file

Writes CDF units

applyCdfGroupFields

Applies a function to a list of fields of each group in a CDF structure

Reads probe-level data ordered as units (probesets) from one or several Affymetrix CEL files

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

Writes BPMAP and TPMAP files.

Gets a subset of groups fields in a CDF structure

Orders the fields according to the value of another field in the same CDF group

Compares the contents of two CDF files

Inverts a read or a write map

readCdfDataFrame

Reads units (probesets) from an Affymetrix CDF file

Copies a CEL file

cdfAddBaseMmCounts

Adds the number of allele A and allele B mismatching nucleotides of the probes in a CDF structure

Gets a subset of groups in a CDF structure

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

Applies a function over the groups in a CDF structure

cdfMergeAlleles

Function to join CDF allele A and allele B groups strand by strand

Reads the QC units of CDF file

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