glm_brainGraphList: Create a graph list with GLM-specific attributes

In brainGraph: Graph Theory Analysis of Brain MRI Data

Description

These methods create a brainGraphList with attributes specific to the results of brainGraph_GLM, mtpc, or NBS. The graphs element of the returned object will contain one graph for each contrast.

Usage

## S3 method for class 'bg_GLM'
make_brainGraphList(x, atlas = x$atlas,
  type = "observed", level = "contrast", set.attrs = FALSE,
  modality = NULL, weighting = NULL, threshold = NULL,
  gnames = x$con.name, ...)

## S3 method for class 'mtpc'
make_brainGraphList(x, atlas = x$atlas,
  type = "observed", level = "contrast", set.attrs = FALSE,
  modality = NULL, weighting = NULL, threshold = NULL,
  gnames = x$con.name, ...)

## S3 method for class 'NBS'
make_brainGraphList(x, atlas, type = "observed",
  level = "contrast", set.attrs = TRUE, modality = NULL,
  weighting = NULL, threshold = NULL, gnames = x$con.name,
  mode = "undirected", weighted = TRUE, diag = FALSE, ...)

Arguments

x	A bg_GLM, mtpc, or NBS object
atlas	Character string specifying the brain atlas to use
type	Character string indicating the type of graphs. Default: observed
level	Character string indicating whether the graphs are subject-, group-, or contrast-specific. Default: 'subject'
set.attrs	Logical indicating whether to assign all graph-, vertex-, and edge-level attributes (via set_brainGraph_attr). Default: TRUE
modality	Character string indicating imaging modality (e.g. 'dti'). Default: NULL
weighting	Character string indicating how the edges are weighted (e.g., 'fa', 'pearson', etc.). Default: NULL
threshold	Integer or number indicating the threshold used when “sparsifying” the connectivity matrix (if any). Default: NULL
gnames	Character vector of graph names (e.g., study IDs if level='subject'). Default: NULL
...	Other arguments passed to set_brainGraph_attr
mode	Character string defining how the matrix should be interpreted. Default: 'undirected'
weighted	Logical specifying whether to create a weighted network
diag	Logical indicating whether to include the diagonal of the connectivity matrix. Default: FALSE

Value

A brainGraphList object, with a graph object for each contrast with additional attributes:

Graph	name (contrast name), outcome (the outcome variable), alpha (the significance level); for MTPC: tau.mtpc, S.mtpc, S.crit, A.crit
Vertex	size2 (t-statistic); size (the t-stat transformed for visualization purposes); p (equal to 1-p); p.fdr (equal to 1-p_{FDR}, the FDR-adjusted p-value); effect.size (the contrast of parameter estimates for t-contrasts; the extra sum of squares for F-contrasts); se (the standard error of gamma); A.mtpc, sig (binary indicating whether A.mtpc > A.crit) (for MTPC)

make_brainGraphList.NBS returns graphs with additional attributes:

Vertex	comp (integer vector indicating connected component membership), p.nbs (P-value for each component)
Edge	stat (the test statistic for each connection), p (the P-value)

Note

Only valid for vertex-level and NBS analyses.

See Also

brainGraph_GLM, mtpc, NBS

Other Graph creation functions: Creating_Graphs, brainGraphList, make_ego_brainGraph

brainGraph documentation built on Oct. 23, 2020, 6:37 p.m.