README.md

In ehfhcrc/UpdateAnno: Update Annotation to Latest Symbols using org.Hs.eq.db

UpdateAnno

Purpose

The UpdateAnno package is designed to ensure that the Gene Symbols used throughout the ImmuneSpace portal are consistent and up to date. There are a number of places where Gene Symbols play an important role: - Gene Expression Explorer - Pulls Gene Symbols from the FeatureAnnotation query - Gene Set Enrichment Analysis - Pulls Gene Symbols from the static gene set module data objects in this package, e.g. chaussabel or emory. - Differential Gene Expression Analysis - Uses the GeneExpressionAnalysisResults query to display differentially expressed genes.

Inner Workings

During installation, the package's vignette updateAnnoGMT.Rmd also installs the latest version of the org.Hs.eq.db R package and uses the ALIAS-to-SYMBOL mapping within org.Hs.eq.db to update the updated_btm_list and updated_btm_df objects in the packages data folder. Since the updating process depends on the vignette, it is important to ensure that the vignette is built during installation.

Use

To install with the vignette: devtools::install_github("RGLab/UpdateAnno", build_vignettes=T)

After installation, a user may access these updated data objects by doing: library(updateAnno)

This will include the data objects in the calling environment.

Then on rsT or rsP, the user should call the runUpdateAnno() function which will do the following: - Update the FeatureAnnotation table with the latest gene symbols - Update the gene expression matrices (flat files / tsv) to use the latest symbols in the summary versions - Update the GeneExpressionAnalysisResults table with newly processed results.

The package also includes two methods that may assist the gene set enrichment analysis process: * UpdateAnnoVec - a function that takes a character vector with gene aliases and maps the aliases to official gene SYMBOLS from the org.Hs.eq.db. * outputUpdatedBTM - a function that writes out a gmt file with the most recently updated BTM object.

ehfhcrc/UpdateAnno documentation built on May 16, 2019, 12:16 a.m.