Tools for masking out problematic Affymetrix probes using VCF files and the oligo Bioconductor package
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README.md

README.md

The oligoMask package DOI

The oligoMask package provides tools for masking out problematic Affymetrix probes using VCF files and the oligo package

It has been established that the presence of single nucleotide variants in transcript regions that are interrogated 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 convenient interface between several packages to facilitate analysis of Affymetrix arrays especially the Gene and Exon varieties. Although, originally designed for the analysis of expression data from mouse recombinant inbred inter-crosses use with human expression arrays is also possible.

Installation

The simplest approach to installing the package is to download and install the files in the latest release either using R CMD INSTALL package_name.tar.gz or via install.packages("package_name.tar.gz", repos=NULL, type="source") from an R session.

The package can also be installed manually by first clicking 'Download ZIP' and unzipping the resulting 'oligoMask-master.zip' file into a convenient directory. From within R in the same directory as 'oligoMask-master' type:

install.packages("oligoMask-master", repos=NULL, type="source")

or for instance using the devtools package:

install_github(username="dbottomly", repo="oligoMask", ref="master")

How to contribute

Contributions are encouraged through the standard fork/pull procedures. Feel free to send me an email with any questions.

Contact

Dan Bottomly bottomly@ohsu.edu