meNet_CGI.RdFor every present CGI, function "meNet_singleCGI" is called and the resulting network is a union of the single-CGI networks. (Optional) weights are chromosomal distances.
meNet_CGI( cg_list = NULL, cgi_list = NULL, link_method = "twoLyr_clust", weighted = TRUE, cor_matrix = NULL, data = NULL, cor_normalization_fun = max_normalization, dist_normalization_fun = neg_max_normalization, cor_threshold = 0.2, neg_cor_threshold = NULL, cor_stDev = NULL, cor_alpha = NULL, n_repetitions = 1000, alternative = "two_sided", infomap_call = "infomap", folder = "./meNet/", file_basename = "meNet_CGI_infomap", relaxation_rate = 0.15, cg_meta = data("CpG_anno450K", package = "meNet"), cg_meta_cols = list(cg_id = "IlmnID", cg_coord = "MAPINFO", island_name = "UCSC_CpG_Islands_Name", island_region = "Relation_to_UCSC_CpG_Island"), include_regions = character(0), expand_cg_list = FALSE, normalization_fun = NULL, save_all_files = FALSE, delete_files = FALSE )
| cg_list | Vector of CpG sites. |
|---|---|
| cgi_list | Vector of CpG islands. |
| link_method | Method used to determine the edges within each CGI subnetwork. See details. Default value is `"twoLyr_clust"`. |
| weighted | Whether the resulting network is weighted. If `TRUE`, the weights are base pair distances between CpGs. Defaults to `TRUE`. |
| cor_matrix | Correlation matrix of CpG sites. |
| data | Data frame with CpGs in columns. Variables in rows are used to calculate `cor_matrix`. |
| cor_normalization_fun | Normalization function for the correlation layer of a CGI. Default method is `max_normalization` function. |
| dist_normalization_fun | Normalization function for the distance layer of a CGI. Default method is `neg_max_normalization` function. |
| cor_threshold | Correlation threshold. Defaults to `0.2`. |
| neg_cor_threshold | Negative correlation threshold. Defaults to `NULL`. |
| cor_stDev | Threshold for the standard deviation of correlation. Defaults to `NULL`. |
| cor_alpha | Significance level of the correlation permutation test. Defaults to `NULL`. |
| n_repetitions | Number of repetitions for resampling and/or for the correlation permutation test. Defaults to `1000`. |
| alternative | Alternative hypothesis for the correlation permutation test. Default value is `"two_sided"`. |
| infomap_call | Path to the `Infomap` on user's system. Default value is `"infomap"`. |
| folder | Folder in which the files will be saved. It is automatically created if not already present. Default value is `"./meNet/"`. |
| file_basename | Base name of the created files. Default value is `"meNet_CGI_infomap"`. If `save_all_files` is `TRUE`, its value changes for every CGI and becomes equal to name of the CGI. |
| relaxation_rate | `multilayer-relax-rate` parameter in `Infomap` call. Defaults to `0.15`. |
| cg_meta | Data frame which defines relationship between CpG sites and CpG islands. It has CpGs in the rows and their description in the columns. If CpG is part of an CGI, `cg_meta` gives the name of the island and the region of an island in which the CpG is found. Additionally, if base pair distances are being calculated, `cg_meta` also holds chromosomal coordinate of CpGs. By default, function uses `CpG_anno450K` data frame which contains Illumina Infinium HumanMethylation450 manifest file. |
| cg_meta_cols | Named list with `cg_meta` column names. The list must include: `cg_id` naming the column with unique CpG names, `island_name` naming the column with CGI names and `island_region` naming the column with the CGI region in which the CpG is located. If base pair distances are being calculated, it should also include `cg_coord` naming the column with chromosomal coordinates. Default value shouldn't be changed if `cg_meta` keeps it default value. |
| include_regions | Regions of CGIs which should be searched for CpGs besides the island itself. Can take any subset of values `"S_Shelf"`, `"S_Shore"`, `"N_Shore"`, `"N_Shelf"`. By default, only the CpGs inside the island are reported. |
| expand_cg_list | Whether, for a CGI containing a CpG from `cg_list`, all CpGs should automatically be added to the network. Default to `FALSE`. |
| normalization_fun | Normalization function applied on the weights of the resulting network, if the network is weighted. |
| save_all_files | Whether all created files should be saved. Defaults to `FALSE`. |
| delete_files | Should created files be automatically deleted from the user's system. Defaults to `FALSE`. If `save_all_files` is `TRUE` then its value is automatically changed to `FALSE.` Changing the parameter to `TRUE` should be done with caution since it will allow the function to delete files from user's system. |
List of nodes can be given either as list of CpGs with parameter `cg_list` or as list of CpG islands with parameter `cgi_list`. In case both lists are given, union of nodes is used.
Passed to meNet_singleCGI `link_method`, `weighted`, `cor_normalization_fun`, `dist_normalization`, `cor_threshold`, `neg_cor_threshold`, `cor_stDev`, `cor_alpha`, `n_repetitions`, `alternative`, `infomap_call`, `folder`, `relaxation_rate`, `cg_meta`, `cg_meta_cols`, `include_regions`, `check_matrices`, `delete_files`