generatePathwaysNetwork: Subnetwork Creation function

Description Usage Arguments Value References Examples

View source: R/generatePathwaysNetwork.R

Description

Subnetwork Creation function

Usage

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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

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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.