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)
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