Man pages for CimpleG
A Method to Identify Single CpG Sites for Classification and Deconvolution
| CimpleG | Find simple CpG (CimpleG) signatures. |
| CimpleG-package | CimpleG: A Method to Identify Single CpG Sites for... |
| compute_ax | Feature selection function used in the sigma delta space |
| compute_diffmeans_sumvar | Compute diff mean sum var dataframe |
| darken | Helper function to darken down a given color. |
| deconvolution_barplot | Stacked barplot of deconvolution results |
| deconvolution_epidish | EpiDISH deconvolution |
| deconvolution_nmf | NMF deconvolution |
| deconvolution_nnls | NNLS deconvolution |
| deconv_pred_obs_plot | Scatter plots of observed (true) vs predicted values for... |
| deconv_ranking_plot | Boxplot and rankings of deconvolution metrics for... |
| diffmeans_sumvariance_plot | Creates the old version of the difference in means by sum of... |
| dmsv_plot | Creates the old version of the difference in means by sum of... |
| eval_test_data | Evaluation of produced models on test data |
| get_cpg_annotation | Get CpG annotation from Illumina |
| lighten | Helper function to lighten up a given color. |
| load_object | Load an R object saved with CimpleG or an RDS file. |
| make_color_palette | Make color palette data frame |
| make_deconv_pred_obs_data | Make tidy data for use in deconvolution plots |
| make_deconv_ref_matrix | Build deconvolution reference matrix |
| predict.CimpleG | Predict outcome from a CimpleG signatures on new data |
| run_deconvolution | Perform deconvolution on a new set of samples, based on the... |
| save_object | Save an R object to disk with fast and efficient compression... |
| select_features | Feature selection function used in the diffmeans, sumvariance... |
| signature_plot | CpG signature plot |
| test_data | Cell line test data |
| test_targets | Cell line test data targets |
| train_data | Cell line train data |
| train_targets | Cell line train data targets |
