A Method to Identify Single CpG Sites for Classification and Deconvolution

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Documentation for package ‘CimpleG’ version 1.0.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

CimpleG	Find simple CpG (CimpleG) signatures.
cimpleg	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
cpg	Find simple CpG (CimpleG) signatures.
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 deconvolution.
deconv_ranking_plot	Boxplot and rankings of deconvolution metrics for deconvolution results.
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