oligo-package: The oligo package: a tool for low-level analysis of...
In jmacdon/oligo: Preprocessing tools for oligonucleotide arrays
Description
Details
Author(s)
References
Description
The oligo package provides tools to preprocess different
oligonucleotide arrays types: expression, tiling, SNP and exon
chips. The supported manufacturers are Affymetrix and NimbleGen.
It offers support to large datasets (when the bigmemory is loaded)
and can execute preprocessing tasks in parallel (if, in addition to
bigmemory, the snow package is also loaded).
Details
The package will read the raw intensity files (CEL for Affymetrix; XYS
for NimbleGen) and allow the user to perform analyses starting at the
feature-level.
Reading in the intensity files require the existence of data packages
that contain the chip specific information (X/Y coordinates; feature
types; sequence). These data packages packages are built using the
pdInfoBuilder package.
For Affymetrix SNP arrays, users are asked to download the already built
annotation packages from BioConductor. This is because these packages
contain metadata that are not automatically created. The following
annotation packages are available:
50K Xba - pd.mapping50kxba.240
50K Hind - pd.mapping50khind.240
250K Sty - pd.mapping250k.sty
250K Nsp - pd.mapping250k.nsp
GenomeWideSnp 5 (SNP 5.0) - pd.genomewidesnp.5
GenomeWideSnp 6 (SNP 6.0) - pd.genomewidesnp.6
For users interested in genotype calls for SNP 5.0 and 6.0 arrays, we
strongly recommend the use use the crlmm package, which implements
a more efficient version of CRLMM.
Author(s)
Benilton Carvalho - carvalho@bclab.org
References
Carvalho, B.; Bengtsson, H.; Speed, T. P. & Irizarry, R. A. Exploration, Normalization, and Genotype Calls of High Density Oligonucleotide SNP Array Data. Biostatistics, 2006.
jmacdon/oligo documentation built on Aug. 11, 2020, 12:32 a.m.
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Description Details Author(s) References
Description
The oligo package provides tools to preprocess different oligonucleotide arrays types: expression, tiling, SNP and exon chips. The supported manufacturers are Affymetrix and NimbleGen.
It offers support to large datasets (when the bigmemory is loaded) and can execute preprocessing tasks in parallel (if, in addition to bigmemory, the snow package is also loaded).
Details
The package will read the raw intensity files (CEL for Affymetrix; XYS for NimbleGen) and allow the user to perform analyses starting at the feature-level.
Reading in the intensity files require the existence of data packages that contain the chip specific information (X/Y coordinates; feature types; sequence). These data packages packages are built using the pdInfoBuilder package.
For Affymetrix SNP arrays, users are asked to download the already built annotation packages from BioConductor. This is because these packages contain metadata that are not automatically created. The following annotation packages are available:
50K Xba - pd.mapping50kxba.240 50K Hind - pd.mapping50khind.240 250K Sty - pd.mapping250k.sty 250K Nsp - pd.mapping250k.nsp GenomeWideSnp 5 (SNP 5.0) - pd.genomewidesnp.5 GenomeWideSnp 6 (SNP 6.0) - pd.genomewidesnp.6
For users interested in genotype calls for SNP 5.0 and 6.0 arrays, we strongly recommend the use use the crlmm package, which implements a more efficient version of CRLMM.
Author(s)
Benilton Carvalho - carvalho@bclab.org
References
Carvalho, B.; Bengtsson, H.; Speed, T. P. & Irizarry, R. A. Exploration, Normalization, and Genotype Calls of High Density Oligonucleotide SNP Array Data. Biostatistics, 2006.
R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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