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R package for sex labeling expression data
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README.md

README.md

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)

Sex labeling genes are from ISEXs (Bongen et al., in preparation).

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