Function reference • 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(): Represent CpGs in the difference in means, sum of variances space. This plot is often used to select CpGs that would be good classifiers. These CpGs are often located on the bottom left and bottom right of this plot.

dmsv_plot(): Represent CpGs in the difference in means, sum of variances space. This plot is often used to select CpGs that would be good classifiers. These CpGs are often located on the bottom left and bottom right of this 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_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