Man pages for xinnyuY/EvoSig
Evolutionary dynamics signature extraction
| Build_post_summary | Build count matrix for input samples |
| ccfMatBuild | Build CCF Matrix for all samples within region 0-upper |
| ccfMatrixBuild | Build count matrix for input samples per cancer type |
| combine_sig_nmf | Combine signatures from different cancer type together |
| cor_facet | Correlation calculation function by group and plot... |
| cor.table | Correlation calculation function |
| EvoSig_input | Produce input ccf count matrix for rank estimate |
| Extract_sig | Perform NMF with consensus signature |
| file_format | Unify format of data frame |
| hc_cluster_test-ccfMat-ccf-matrix-for-all-samples | Perform Hierarchical clustering number estimate |
| hc_combine_sig-Combine-signatures-and-estimate-number-of-clusters | Combine signatures and estimate number of clusters |
| hc_consensus-ccfMat-ccf-matrix-for-all-samples | Plotting for HC results |
| immune_landscape_measure | Immune landscape measures dataset |
| load_ccf | Load multiple format ccf file |
| multi.dir.create | create multiple dir |
| nmf_sig_all_plot | Perform nmf for multiple cancer types |
| nmf_sig_plot_type | Perform nmf for a cancer type |
| ParseSnvCnaPcawgFormat | Merge ssm and cna files |
| rank_estimate_plot | Plotting rank estimate |
| scatter_facet | Plot scatterplot for specific measure with evo sig and... |
| sig_plot | Plot signature matrix |
| strip_color | Customize top strip color |
| TCGAtypefile | TCGAtypefile dataset |
