exprsex

E Flynn and Annie Chang

R package for sex labeling expression data. Still beta version.

To install, in R

1. Install three Bioconductor packages for data mapping: BiocManager::install(c("org.Hs.eg.db", "org.Rn.eg.db", "org.Mm.eg.db"))
2. Make sure you have devtools installed and loaded, then run: devtools::install_github(erflynn/exprsex). This will also prompt you to install the required dependencies.

To run:

1. Download an expression dataset using getPrepGSE(gse)
2. Prepare the input by running: reorderRank(expr)
3. Then, either:
   • Train a sex labeler: fit <- trainSexLab(expr, sex_lab)
   • Or run sex labeling: predSexLab(fit, expr) the default fit can be accessed with data(default_fit)

For a full example, see vignettes/sex-label-vignette.Rmd.

We also provide code to map a wide range of GEO platforms to entrez IDs in gpl_map() functions. This is done as part of the getPrepGSE function. To map an individual platform: ref_tab <- parse_entrez_from_gpl(platform_id)