Package index • CimpleG

All functions

CimpleG() cimpleg() cpg(): Find simple CpG (CimpleG) signatures.

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.

deconv_pred_obs_plot(): Scatter plots of observed (true) vs predicted values for deconvolution.

deconv_ranking_plot(): Boxplot and rankings of deconvolution metrics for deconvolution results.

deconvolution_barplot(): Stacked barplot of deconvolution results

deconvolution_epidish(): EpiDISH deconvolution

deconvolution_nmf(): NMF deconvolution

deconvolution_nnls(): NNLS deconvolution

diffmeans_sumvariance_plot(): Creates the old version of the difference in means by sum of variances plot

dmsv_plot(): Creates the old version of the difference in means by sum of variances plot

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 CimpleG models trained

save_object(): Save an R object to disk with fast and efficient compression algorithms.

select_features(): Feature selection function used in the diffmeans, sumvariance space

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