BiOFI (version 0.1.0)

IIS: IIS

Description

A function is used to calculates and identify the key nodes,the formula of IIS is: IIS= nDFS x DFS + nDS x DS + nES x ES + nAS x AS; nDFS,nDS,nES,nAS indict the weight value of DFS,DS,ES and AS, and nDFS + nDS + nES + nAS = 1; DFS means Difference Score; DS means Degree Score; ES means Edge Score; AS means Abundance Score.

Usage

IIS(
  microApath,
  metaApath,
  conf = NULL,
  groupInfo = NULL,
  nDFS = 0.4,
  nDS = 0.3,
  nES = 0.2,
  nAS = 0.1,
  NS = 2.5,
  r = 0.5,
  p_adjust = 0.05
)

Value

IIS_res A list including IIS and other sub-score results.

Arguments

microApath

A data frame including microbes and predicted KEGG pathways.

metaApath

A data frame including metabolites with compound ID and predicted KEGG pathways from Meta2pathway function.

conf

A data frame including confounders. Default value is NULL.

groupInfo

A data frame including sample grouping information

nDFS

A value indicated the weight of difference Score in the IIS formula. Default value is 0.4.

nDS

A value indicated the weight of degree score in the IIS formula. Default value is 0.3.

nES

A value indicated the weight of edge score in the IIS formula. Default value is 0.2.

nAS

A value indicated the weight of abundance score in the IIS formula. Default value is 0.1.

NS

A threshold value of IIS to identify the key nodes. Default value is 2.5.

r

A threshold value of correlation coefficient to construct the network. Default value is 0.5.

p_adjust

A threshold value of correlation adjust p value to construct the network. Default value is 0.05.

Examples

IIScore <- IIS(microApath = micro.eg, metaApath = metabo.eg,
               conf = confounder.eg, groupInfo = groupInfo.eg)