generatePathwaysNetwork: Subnetwork Creation function

In krumsieklab/MoDentify: Phenotype-driven module identification

Description

Subnetwork Creation function

Usage

generatePathwaysNetwork(data, covars = NULL, annotations,
  level = "Sub.pathway", correlation.type = "partial", alpha = 0.05,
  correction.method = "bonferroni", rm.unknown = TRUE,
  representative.method = "eigenmetabolite")

Arguments

data	a data.table or matrix containing data. The columns correspond to the variables, the rows to the observations.
covars	a data.table containing covariates to correct for. The columns correspond to the different covariates, the rows to the observations.
annotations	a data.table containing annotations for the variables. The columns correspond to the different annotations, the rows to the variables.
level	name of the column that should be used for grouping the variables. The default is "SUB_PATHWAY".
correlation.type	type of correlation to be estimated. Can either be "pearson", or "partial".
alpha	significance threshold (type 1 error) for multiple testing correction.
correction.method	the method that should be used for multiple testing correction ("bonferroni", "BH", "BY", "fdr", "holm", "hochberg", "hommel", "none"). Default is bonferroni. See p.adjust.
rm.unknown	remove variables, for which the group is unknown. The corresponding grouping variable name should be "Unknown". Default is TRUE.
representative.method	the method, that is used for calculation of the eigenmetabolites. Currently implemented: "eigenmetabolite" and "average"

Value

a list with a network containing the variables as nodes as an igraph object and a list with the module representatives including their explained variances.

References

\insertRef

Krumsiek2011MoDentify

\insertRef

Do2017MoDentify

Examples

data(qmdiab.data)
data(qmdiab.annos)

pathway.graph <- generatePathwaysNetwork(
  data = qmdiab.data,
  annotations = qmdiab.annos, level = "Sub.pathway"
)

krumsieklab/MoDentify documentation built on March 24, 2021, 9:01 p.m.