README.md

In harrisgm/clarioms.mouse.probeFile: Probe sequence data for microarrays of type clarioms.mouse

clariomS.mouse.probeFile

Contains annotated probe-level information for the ClariomS mouse microarray. Used by the GCSscore R package for differential gene expression analysis.

Description

===================

The clariomS.mouse.probeFile package is an AnnotationForge-generated package containing the probe sequence information for ClariomS mouse array. The package contains a data.frame containing the necessary probe-level information to run the GCSscore differential expression on the following Affymetrix/Thermo-Fisher cchip type:

ClariomS mouse microarray

All probe-level information in this file was pulled from the platform design (pd) annotation package (pd.clariom.s.mouse) on Bioconductor: https://bioconductor.org/packages/release/data/annotation/html/pd.mta.1.0.html

This probe-level package was created using the AnnotationForge package. The AnnotationForge package required the getProbeDataAffy function to be modified to correctly read in the probeFile file for newer Affymetrix array types. This modified function was saved as getProbeDataMTA. The customized functions from the AnnotationForge package can be found the following github repository: https://github.com/harrisgm/GCSscore-probeFile-functions

Additionally, the compression scheme of the rda file was set to xz with a compression level of 9.

The only column that is not directly from the platform design (pd) packages is the GC.Count column was generated by running the following commands on the full probe sequences that are pulled from the platform design packages (found in the ClariomSpFBuilder.R functions in the GCSscore-probeFile-functions repository:

chip.pmfeature[,GC.count := str_count(sequence, "G|C")]

The full probe sequence column is retained and the GC.count column is added to the data.frame object. The full probe sequence column can be retained due to the small file sizes of the ClariomS probe-level data.

Installation

clariomS.mouse.probeFile is an package that is in the process being uploaded to the BioConductor repository. Until it is uploaded to Bioconductor, the recommended way to install it is to load R and ensure that all dependencies are install prior to installation.

Dependencies from Bioconductor (run commands in Rstudio/R.app):

```r
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("AnnotationDbi")

Once the dependencies are installed, build and install the clariomS.mouse.probeFile package from source.

Contact

Guy Harris, M.S. [e-mail]

Michael F. Miles, M.D., Ph.D. [e-mail]

harrisgm/clarioms.mouse.probeFile documentation built on Nov. 4, 2019, 1:28 p.m.