meNet_CGI: CpG network: edges are based on CpG island affiliation
In ivabudimir/meNet: Correlation-based network analysis of methylation data

For 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'

ivabudimir/meNet documentation built on Dec. 20, 2021, 8:03 p.m.