Man pages for tanaylab/methylayer
Layered modeling of tumor methylation
| calc_gene_cor_before_after_deconv | calculate expression of loci to specific genes before and... |
| cis_em_genomic | Get candidates non-promoter cis regulation |
| cis_em_promoters | Get candidates for promoters that are regulated by... |
| cluster_em_cross_cor | Cluster Expression-methylation cross-correlation |
| coord_to_promoter_names | Change rownames of matrix from coordinates to promoter names |
| deconv_TME | Deconvolute TME (tumor microenvironment) effects from... |
| em_cross_cor | Calculate Expression-methylation cross-correlation |
| export_em_cross_mods | Export Expression-methylation cross-correlation clustering to... |
| feats_to_knn_matrix | Calculate knn-matrix based on feature matrix |
| gene_promoter_cors | Get correlations of all promoters to a specific gene |
| get_TME_genes | Extract TME genes from methylation expression clustering |
| immune_cafs_signature_from_clust | Define immune and CAF signatures |
| intervs_to_mat | Transform an intervals set to matrix |
| mat_to_intervs | Transform a matrix with coordinate rownames to intervals set |
| methylayer-package | methylayer: Layered modeling of tumor methylation |
| normalize_immune_cafs_meth | Normalize methylation matrix for immune and CAF signatures |
| normalize_mat_knn | Normalize matrix using knn-matrix |
| null-default | Default value for 'NULL'. |
| pipe | Pipe operator |
| plot_em_cross_cor | Plot clustered Expression-methylation cross-correlation... |
| plot_norm_vs_raw_gene_scatter | Plot scatter of raw expression-methylation correaltion vs... |
| shuffle_each_column | Shuffles each column of a numeric matrix |
