Man pages for ivabudimir/meNet
Correlation-based network analysis of methylation data
| Bacalini_betaValues | Bacalini HM450K methylation data |
| Bacalini_sampleSheet | Bacalini sample sheet |
| boxed_heatmap | Heat map without the use of 'layout' function |
| coord_sort | Sorting CpGs by coordinate |
| cor_permutationTest | Correlation permutation test |
| cor_resamplingStats | Mean and standard deviation of correlation |
| CpG_annoHM450K | Description of HM450K CpG sites |
| CpG_genes | Genes associated with HM450K CpG sites |
| CpG_in_CGI | CpGs within a CpG island |
| find_CpG | CpG coordinates on a chromosome |
| Johansson_residuals | Johansson HM450K methylation data |
| max_normalization | Maximum normalization |
| meMultiplex | Multiplex: 'meNet' file from two 'igraph' layers |
| meMultiplex_communities | Multiplex community structure |
| meMultiplex_to_multinet | Multiplex: 'meNet' file to 'multinet' object |
| meNet_CGI | CpG network: edges are based on CpG island affiliation |
| meNet_cor | CpG network: edges based on correlation |
| meNet_gene | CpG network: edges are based on gene affiliation |
| meNet_singleCGI | CpG network for a single CpG island |
| meNet_singleGene | CpG network for a single gene |
| neg_max_normalization | Negative maximum normalization |
| N_ranges | Unsequences genome |
| plotCI_meCGI | Beta value error plot for a CpG island |
| plotCI_meCpG | Beta value error plot with CpG coordinates |
| plot_multiplex | Multiplex plot |
| read_infomap_communities | Multiplex community structure from file |
| UCSC_CGI | UCSC CpG islands |
| UCSC_genes | UCSC transcripts |
