# corr.matrix: Calculate correlation matrix and threshold In brainGraph: Graph Theory Analysis of Brain MRI Data

## Description

`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.

## Usage

 ```1 2``` ```corr.matrix(resids, densities, thresholds = NULL, what = c("resids", "raw"), exclude.reg = NULL, type = c("pearson", "spearman"), rand = FALSE) ```

## Arguments

 `resids` An object of class `brainGraph_resids` (the output from `get.resid`) `densities` Numeric vector indicating the resultant network density(ies); keeps the top X% of correlations `thresholds` Numeric; absolute correlation value to threshold by (default: `NULL`) `what` Character string indicating whether to correlate the residuals or the raw structural MRI values (default: `'resids'`) `exclude.reg` Character vector of regions to exclude (default: `NULL`) `type` Character string indicating which type of correlation coefficient to calculate (default: `'pearson'`) `rand` Logical indicating whether the function is being called for permutation testing; not intended for general use (default: `FALSE`)

## Details

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.

## Value

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 p-values. `r.thresh` A 3-d 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

## Author(s)

Christopher G. Watson, [email protected]

`rcorr`

Other Structural covariance network functions: `IndividualContributions`, `brainGraph_boot`, `brainGraph_init`, `brainGraph_permute`, `get.resid`, `plot.brainGraph_resids`, `plot_volumetric`

## Examples

 ```1 2 3 4 5``` ```## Not run: myResids <- get.resid(lhrh, covars) corrs <- corr.matrix(myResids, densities=densities))) ## End(Not run) ```

brainGraph documentation built on May 29, 2018, 9:03 a.m.