get_IMON: get_IMON

In LucaAnholt/PanViz: Integrating Multi-Omic Network Data With Summay-Level GWAS Data

get_IMON

Description

Internal function that constructs an IMON (Integrated Multi-Omic Network) for an inputted vector of SNPs and exports an igraph file.

Usage

get_IMON(
  snp_list,
  ego = 5,
  save_file = c(FALSE, TRUE),
  export_type = c("igraph", "edge_list", "graphml", "gml"),
  directory = c("wd", "choose"),
  progress_bar = c(TRUE, FALSE)
)

Arguments

snp_list	A vector of SNPs (strings/characters) using standard NCBI dbSNP accession number naming convention (e.g. "rs185345278")
ego	This dictates what length order ego-centred network should be constructed. If set to 5 (default and recommended), an IMON with the first layer of the connected metabolome will be returned. If set above 5, the corresponding extra layer of the metabolome will be returned. If set to 0 (not recommended) the fully connected metabolome will be returned. Note, this cannot be set between 0 and 5.
save_file	Boolean (default = FALSE) argument that indicates whether or not the user wants to save the graph as an exported file in their current working directory
export_type	This dictates the network data structure saved in the chosen directory. By default this outputs an igraph object, however, you can choose to export and save an edge list, graphml or GML file.
directory	If set to "choose" this argument allows the user to interactively select the directory of their choice in which they wish to save the constructed IMON, else the file will be saved to the working directory "wd" by default
progress_bar	Boolean (default = TRUE) argument that controls whether or not a progress bar for calculations/KEGGREST API GET requests should be printed to the console

Value

An igraph object containing the constructed IMON

Examples

##getting vector of SNPs to query:
data("er_snp_vector")
##build IMON using vector:
G <- PanViz::get_IMON(snp_list = er_snp_vector, ego = 5, save_file = FALSE)

LucaAnholt/PanViz documentation built on April 17, 2022, 7:28 a.m.