Author: Tiago Maié
Date: 2025-12-05

# Generate signatures

#### Tiago Maié

#### 2025-12-05

## CimpleG (Simple CpG signatures)

- CimpleG tries to find the CpGs that best classify a cell-type given a train dataset
- It also enables you to perform cell-type deconvolution in a couple of easy steps
- It can use beta or M values
- Here we show how easy it is to generate a signatures

### Installation

If you haven’t installed CimpleG, you can find the instructions to do so here. However it should be as simple as:

    if (!require("CimpleG")) devtools::install_github("costalab/CimpleG")

### Loading package

We load the CimpleG package.

    library("CimpleG")
    #> ---------------------
    #> CimpleG version 1.0.1
    #> ---------------------

### Loading data

In this tutorial, we will use a small dataset with just 409 samples and 1000 CpGs. We will also use a table with metadata regarding these samples. This dataset comes included with CimpleG. You can read more about it here: .

    # load data
    data(train_data)
    data(train_targets)

### Running CimpleG

Running CimpleG can be quite simple. You just need to run the CimpleG function with a few parameters.

    # run CimpleG
    cimpleg_result <- CimpleG(
      train_data,
      train_targets,
      target_columns = c("blood_cells", "hepatocytes"),
      train_only = TRUE
    )
    #> Training for target 'blood_cells' with 'CimpleG' has finished.: 1.643 sec elapsed
    #> Training for target 'hepatocytes' with 'CimpleG' has finished.: 0.453 sec elapsed

Here we are generating signatures to find leukocytes and hepatocytes.

### Plotting CimpleG CpG signature

We can quickly visualize how our signature is able to separate the data.

    sig_plt <-
      signature_plot(
        cimpleg_result,
        train_data,
        train_targets,
        sample_id_column = "gsm",
        true_label_column = "cell_type"
      )
    sig_plt$plot