Description Usage Arguments Value Note See Also
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17  ## 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, ...)

x 
A 
atlas 
Character string specifying the brain atlas to use 
type 
Character string indicating the type of graphs. Default:

level 
Character string indicating whether the graphs are subject,
group, or contrastspecific. Default: 
set.attrs 
Logical indicating whether to assign all graph, vertex,
and edgelevel attributes (via 
modality 
Character string indicating imaging modality (e.g. 'dti').
Default: 
weighting 
Character string indicating how the edges are weighted
(e.g., 'fa', 'pearson', etc.). Default: 
threshold 
Integer or number indicating the threshold used when
“sparsifying” the connectivity matrix (if any). Default: 
gnames 
Character vector of graph names (e.g., study IDs if

... 
Other arguments passed to 
mode 
Character string defining how the matrix should be interpreted.
Default: 
weighted 
Logical specifying whether to create a weighted network 
diag 
Logical indicating whether to include the diagonal of the
connectivity matrix. Default: 
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 (tstatistic); size (the tstat
transformed for visualization purposes); p (equal to 1p);
p.fdr (equal to 1p_{FDR}, the FDRadjusted pvalue);
effect.size (the contrast of parameter estimates for tcontrasts;
the extra sum of squares for Fcontrasts); se (the
standard error of gamma); A.mtpc, sig (binary
indicating whether 
make_brainGraphList.NBS
returns graphs with additional
attributes:
Vertex 
comp (integer vector indicating connected component membership), p.nbs (Pvalue for each component) 
Edge 
stat (the test statistic for each connection), p (the Pvalue) 
Only valid for vertexlevel and NBS analyses.
Other Graph creation functions: Creating_Graphs
,
brainGraphList
,
make_ego_brainGraph
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