This vignette is the landing page for omics-related utilities in
Rtoolset. It provides a short overview of the available
helpers and points to the more focused RNA-seq and DNA methylation
tutorials.
Overview
Rtoolset currently includes lightweight helpers for a
few common preprocessing tasks across omics workflows:
- filtering and normalizing RNA-seq count matrices
- log transformation and feature ranking
- converting DNA methylation beta values to M values
These functions are designed to plug into larger workflows built with
packages such as edgeR and limma.
Available Tutorials
RNA-seq Utilities
The RNA-seq tutorial covers:
-
filter_calcpm_dge()for filtering and CPM calculation -
log_transform()for custom transformations -
get_top_var_mat()for selecting highly variable features
See the RNA-seq Utilities vignette for examples and a suggested preprocessing workflow.
DNA Methylation Utilities
The DNA methylation tutorial focuses on:
-
beta2M()for converting beta values to M values
See the DNA Methylation Utilities vignette for examples, the conversion formula, and downstream analysis notes.
Function Map
| Function | Typical use |
|---|---|
filter_calcpm_dge() |
RNA-seq filtering, normalization, and CPM workflow |
log_transform() |
Custom log transformation of count-like data |
get_top_var_mat() |
Selecting highly variable features for exploration |
beta2M() |
Converting methylation beta values to M values |
Choosing a Tutorial
- Start with RNA-seq Utilities if you are working with raw count matrices.
- Start with DNA Methylation Utilities if you are working with beta values from methylation assays.
- Return to this page when you want a compact overview of omics-related helpers in the package.