Description Usage Arguments Details Value Author(s) See Also Examples
corr.matrix
calculates the correlation between all column pairs of a
given data frame, and thresholds the resultant correlation matrix based on a
given density (e.g., 0.1
if you want to keep only the 10% strongest
correlations). If you want to threshold by a specific correlation coefficient
(via the thresholds
argument), then the densities
argument is
ignored.
1 2 
resids 
An object of class 
densities 
Numeric vector indicating the resultant network density(ies); keeps the top X% of correlations 
thresholds 
Numeric; absolute correlation value to threshold by
(default: 
what 
Character string indicating whether to correlate the residuals or
the raw structural MRI values (default: 
exclude.reg 
Character vector of regions to exclude (default:

type 
Character string indicating which type of correlation coefficient
to calculate (default: 
rand 
Logical indicating whether the function is being called for
permutation testing; not intended for general use (default: 
If you wish to exclude regions from your analysis, you can give the indices
of their columns with the exclude.reg
argument.
By default, the Pearson correlation coefficients are calculated, but you can
return Spearman by changing the type
argument.
A nested list containing a list for all subject groups; each of these has the following components:
R 
Numeric matrix of correlation coefficients. 
P 
Numeric matrix of pvalues. 
r.thresh 
A 3d binary array indicating correlations that are above a certain threshold. The length of the 3rd dimension equals the number of thresholds/densities supplied. 
thresholds 
Numeric vector; the thresholds supplied. 
densities 
Numeric vector; the densities supplied. 
what 
Residuals or raw values 
exclude.reg 
Excluded regions (if any) 
type 
Pearson or Spearman 
Christopher G. Watson, [email protected]
Other Structural covariance network functions: IndividualContributions
,
brainGraph_boot
,
brainGraph_init
,
brainGraph_permute
,
get.resid
,
plot.brainGraph_resids
,
plot_volumetric
1 2 3 4 5  ## Not run:
myResids < get.resid(lhrh, covars)
corrs < corr.matrix(myResids, densities=densities)))
## End(Not run)

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