It has been established that the presence of single nucleotide variants in transcript regions that are interograted by microarray probes can cause spurious decreases in signal. In the case of Affymetrix arrays, more than one probe is present in a given probeset/transcript-cluster and this provides the opportunity to remove probes that could potentially be affected prior to background correction, normalization and summarization as in the RMA method. This package is intended to provide the user a convient interface between several packages to faciliate analysis of Affymetrix arrays especially the Gene and Exon varieties. Although, originally designed for the analysis of expression data from mouse recombinant inbred intercrosses use with human expression arrays is also possible.
|Imports:||methods, DBI, RSQLite,VariantAnnotation,batch,reshape2,graph,RBGL,oligo,oligoClasses,BSgenome,Biostrings,seqnames.db|
|Depends:||R (>= 3.0.0)|
|Suggests:||RUnit, BiocGenerics, BSgenome.Mmusculs.UCSC.mm9|
|Collate:||helper_functions.R tableSchemaList.R vcf_parsing.R VariantMaskParams.R|
|Built:||R 3.0.0; ; 2013-06-10 21:05:11 UTC; unix|
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TableSchemaList-class Class '"TableSchemaList"' VariantMaskParams-class Class '"VariantMaskParams"' VcfDB-class Class '"VcfDB"' maskRMA Method implementing variant masking along with the RMA algorithm create.sanger.mouse.vcf.db A function for the conversion of Sanger VCF files to an SQLite database om.db.file Function returning a path to a sample oligoMask SQLite database om.tab.file Function returning a path to a sample tab-delimited probe sequence file from Affymetrix om.vcf.file Function returning a path to a subset of a Sanger VCF file containing SNVs for several mouse inbred strains. om.lo.file Function returning a path to the lifted over coordinates from the om.tab.file test.pd.1.0.st.v1 A small sample 'AffyGenePDInfo' class for testing purposes SunGeneFS A subset of the Affy Gene ST expression data from Sun et al. 2012
Further information is available in the following vignettes:
Maintainer: Daniel Bottomly <[email protected]>
Sun, Wei, et al. "Transcriptome atlases of mouse brain reveals differential expression across brain regions and genetic backgrounds." G3: Genes| Genomes| Genetics 2.2 (2012): 203-211.
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