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calc_gene_cor_before_after_deconv()
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calculate expression of loci to specific genes before and after TME deconvolution |
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cis_em_genomic()
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Get candidates non-promoter cis regulation |
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cis_em_promoters()
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Get candidates for promoters that are regulated by methylation in cis |
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cluster_em_cross_cor()
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Cluster Expression-methylation cross-correlation |
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coord_to_promoter_names()
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Change rownames of matrix from coordinates to promoter names |
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deconv_TME()
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Deconvolute TME (tumor microenvironment) effects from methylation data |
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em_cross_cor()
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Calculate Expression-methylation cross-correlation |
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export_em_cross_mods()
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Export Expression-methylation cross-correlation clustering to excel sheet |
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feats_to_knn_matrix()
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Calculate knn-matrix based on feature matrix |
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gene_promoter_cors()
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Get correlations of all promoters to a specific gene |
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get_TME_genes()
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Extract TME genes from methylation expression clustering |
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immune_cafs_signature_from_clust()
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Define immune and CAF signatures |
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intervs_to_mat()
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Transform an intervals set to matrix |
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mat_to_intervs()
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Transform a matrix with coordinate rownames to intervals set |
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normalize_immune_cafs_meth()
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Normalize methylation matrix for immune and CAF signatures |
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normalize_mat_knn()
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Normalize matrix using knn-matrix |
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plot_em_cross_cor()
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Plot clustered Expression-methylation cross-correlation matrix |
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plot_norm_vs_raw_gene_scatter()
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Plot scatter of raw expression-methylation correaltion vs normalized for specific genes |
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shuffle_each_column()
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Shuffles each column of a numeric matrix |