individ_contrib: Approaches to estimate individual network contribution

In brainGraph: Graph Theory Analysis of Brain MRI Data

Description

loo calculates the individual contribution to group network data for each subject in each group using a “leave-one-out” approach. The residuals of a single subject are excluded, and a correlation matrix is created. This is compared to the original correlation matrix using the Mantel test.

aop calculates the individual contribution using an “add-one-patient” approach. The residuals of a single patient are added to those of a control group, and a correlation matrix is created. This is repeated for all individual patients and each patient group.

The summary method prints the group/region-wise means and standard deviations.

The plot method is only valid for regional contribution estimates, and plots the average regional contribution for each vertex/region.

Usage

loo(resids, corrs, level = c("global", "regional"))

aop(resids, corrs, level = c("global", "regional"), control.value = 1L)

## S3 method for class 'IC'
summary(object, region = NULL, digits = max(3L,
  getOption("digits") - 2L), ...)

## S3 method for class 'IC'
plot(x, plot.type = c("mean", "smooth", "boxplot"),
  region = NULL, ids = TRUE, ...)

Arguments

resids	An object of class brainGraph_resids (the output from get.resid)
corrs	List of lists of correlation matrices (as output by corr.matrix).
level	Character string; the level at which you want to calculate contributions (either global or regional)
control.value	Integer or character string specifying the control group (default: 1L)
object, x	A IC object
region	Character vector specifying which regions' IC's to print. Only relevant if method='Leave one out'
digits	Integer specifying the number of digits to display for P-values
...	Unused
plot.type	Character string indicating the type of plot; the default is to plot the mean (along with standard errors)
ids	Logical indicating whether to plot Study ID's for outliers. Otherwise plots the integer index

Value

A data.table with columns for

Study.ID	Subject identifier
Group	Group membership
region	If level='regional'
IC,RC	The value of the individual/regional contributions

Note

For aop, it is assumed by default that the control group is the first group.

Author(s)

Christopher G. Watson, [e-mail]

References

Saggar, M. and Hosseini, S.M.H. and Buno, J.L. and Quintin, E. and Raman, M.M. and Kesler, S.R. and Reiss, A.L. (2015) Estimating individual contributions from group-based structural correlations networks. NeuroImage, 120, 274–284. https://dx.doi.org/10.1016/j.neuroimage.2015.07.006

See Also

Other Structural covariance network functions: Bootstrapping, Residuals, brainGraph_permute, corr.matrix, import_scn, plot_volumetric

Examples

## Not run: 
IC <- loo(resids.all, corrs)
RC <- loo(resids.all, corrs, level='regional')

## End(Not run)
## Not run: 
IC <- aop(resids.all, corrs)
RC <- aop(resids.all, corrs, level='regional')

## End(Not run)

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