Package index • methyldeconv

All functions

check_input(): Check input matrices

check_input_beta(): Check input beta matrix

check_input_mset(): Check input methylSet

create_beta(): Create beta matrix from a methylset matrices

deconvolute(): Deconvolution with methyldeconv

deconvolute_combined(): Run selected set of methods and average results

deconvolution_methods: List of supported deconvolution methods

get_epidish_signature_matrix(): Get EpiDISH Signature Matrix

get_houseman_signature_matrix(): Get Houseman Signature Matrix

get_methatlas_signature_matrix(): Get MethAtlas Signature Matrix

get_methylcc_signature_matrix(): Get MethylCC Signature Matrix (DMRs)

get_methylresolver_signature_matrix(): Get MethylResolver Signature Matrix

init_python(): Initialize Python Environment with Miniconda

methyldeconvstartup: Manage python dependencies according to: https://rstudio.github.io/reticulate/articles/python_dependencies.html#manual-configuration

normalize_deconv_results(): Normalize deconvolution result

rename_cell_types(): Rename Cell Types in Deconvolution Results

results_aggregated_boxplot(): Function to plot aggregated deconvolution results as boxplots for each cell type and method

results_barplot(): Function to plot deconvolution results as barplots for each sample

results_boxplot(): Function to plot deconvolution results as boxplots for each cell type

run_epidish(): run EpiDISH

run_houseman(): Run the improved Houseman method

run_methatlas(): run MethAtlas

run_methylcc(): run methylCC deconvolution

run_methylresolver(): Run MethylResolver