Package: affxparser 1.79.0

Kasper Daniel Hansen

affxparser: 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.

Authors:Henrik Bengtsson [aut], James Bullard [aut], Robert Gentleman [ctb], Kasper Daniel Hansen [aut, cre], Jim Hester [ctb], Martin Morgan [ctb]

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affxparser.pdf |affxparser.html✨
affxparser/json (API)
NEWS

# Install 'affxparser' in R:
install.packages('affxparser', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/henrikbengtsson/affxparser/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On BioConductor:affxparser-1.79.0(bioc 3.21)affxparser-1.78.0(bioc 3.20)

infrastructuredataimportmicroarrayproprietaryplatformsonechannelbioconductorcpp

8.83 score 7 stars 15 packages 65 scripts 2.4k downloads 13 mentions 65 exports 0 dependencies

Last updated 2 months agofrom:25ddf5a692. Checks:OK: 1 WARNING: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 10 2024
R-4.5-win-x86_64WARNINGOct 30 2024
R-4.5-linux-x86_64WARNINGOct 30 2024
R-4.4-win-x86_64WARNINGDec 10 2024
R-4.4-mac-x86_64WARNINGDec 10 2024
R-4.4-mac-aarch64WARNINGDec 10 2024
R-4.3-win-x86_64WARNINGDec 10 2024
R-4.3-mac-x86_64WARNINGDec 10 2024
R-4.3-mac-aarch64WARNINGDec 10 2024

Exports:applyCdfBlocksapplyCdfGroupFieldsapplyCdfGroupsarrangeCelFilesByChipTypecdfAddBaseMmCountscdfAddPlasqTypescdfAddProbeOffsetscdfGetFieldscdfGetGroupscdfGtypeCelToPQcdfHeaderToCelHeadercdfMergeAllelescdfMergeStrandscdfMergeToQuartetscdfOrderBycdfOrderColumnsBycdfSetDimensioncompareCdfscompareCelsconvertCdfconvertCelcopyCelcreateCelfindCdffindFilesinvertMapisCelFileparseDatHeaderStringreadBpmapreadBpmapHeaderreadBpmapSeqinforeadCcgreadCcgHeaderreadCdfreadCdfCellIndicesreadCdfDataFramereadCdfGroupNamesreadCdfHeaderreadCdfIsPmreadCdfNbrOfCellsPerUnitGroupreadCdfQcreadCdfUnitNamesreadCdfUnitsreadCdfUnitsWriteMapreadCelreadCelHeaderreadCelIntensitiesreadCelRectanglereadCelUnitsreadChpreadClfreadClfEnvreadClfHeaderreadPgfreadPgfEnvreadPgfHeadertpmap2bpmapupdateCelupdateCelUnitswriteCdfwriteCdfHeaderwriteCdfQcUnitswriteCdfUnitswriteCelHeaderwriteTpmap

Dependencies:

Readme and manuals

Help Manual

Help pageTopics
Package affxparseraffxparser-package affxparser
1. Dictionary1. Dictionary
2. Cell coordinates and cell indices2. Cell coordinates and cell indices
Applies a function to a list of fields of each group in a CDF structureapplyCdfGroupFields
Applies a function over the groups in a CDF structureapplyCdfBlocks applyCdfGroups
Compares the contents of two CDF filescompareCdfs
Compares the contents of two CEL filescompareCels
Converts a CDF into the same CDF but with another formatconvertCdf
Converts a CEL into the same CEL but with another formatconvertCel
Creates an empty CEL filecreateCel
Search for CDF files in multiple directoriesfindCdf
Parses a Bpmap filereadBpmap readBpmapHeader readBpmapSeqinfo
Reads an Affymetrix Command Console Generic (CCG) Data filereadCcg
Reads an the header of an Affymetrix Command Console Generic (CCG) filereadCcgHeader
Reads (one-based) cell indices of units (probesets) in an Affymetrix CDF filereadCdfCellIndices
Reads group names for a set of units (probesets) in an Affymetrix CDF filereadCdfGroupNames
Reads the header associated with an Affymetrix CDF filereadCdfHeader
Reads unit (probeset) names from an Affymetrix CDF filereadCdfUnitNames
Reads units (probesets) from an Affymetrix CDF filereadCdfUnits
Reads an Affymetrix CEL filereadCel
Parsing the header of an Affymetrix CEL filereadCelHeader
Reads the intensities contained in several Affymetrix CEL filesreadCelIntensities
Reads a spatial subset of probe-level data from Affymetrix CEL filesreadCelRectangle
Reads probe-level data ordered as units (probesets) from one or several Affymetrix CEL filesreadCelUnits
A function to read Affymetrix CHP filesreadChp
Parsing a CLF file using Affymetrix Fusion SDKreadClf
Parsing a CLF file using Affymetrix Fusion SDKreadClfEnv
Read the header of a CLF file.readClfHeader
Parsing a PGF file using Affymetrix Fusion SDKreadPgf
Parsing a PGF file using Affymetrix Fusion SDKreadPgfEnv
Read the header of a PGF file into a list.readPgfHeader
Updates a CEL fileupdateCel
Updates a CEL file unit by unitupdateCelUnits
Writes BPMAP and TPMAP files.tpmap2bpmap writeTpmap