permuco4brain provides functions to compute permutation test in brain imagery data. It is designed for M-EEG/ERP data.
permuco4brain is an add-on to
permuco to computing cluster-mass tests, the “threshold-free clusters-enhancement” and the Troendle’s procedure for tests distribution in space and time (e.g.: full-scalp EEG data).
permuco4brain currently works jointly with
permuco 1.1.1 (github). Download it using:
devtools::install_github("jaromilfrossard/permuco", build_vignettes = TRUE)
permuco4brain is still under development and you can expect changes. Make sure to install
permuco4brain with its full documentation:
devtools::install_github("jaromilfrossard/permuco4brain", build_vignettes = TRUE)
The main function of
brainperm() and it needs:
formula: a formula object defining the design (right side) and a 3D array containing the signals (left side). The signal is a 3D array visible in the global environment. Its dimension is the design X samples X channels. Each “rows” of the 3D array should be related to the corresponding row of the design (
data: a dataframe containing the variables of the design.
igraphobject defining spatial adjacency of the channels (third dimension of the signal). The names of the vertices should correspond to the names of the 3rd dimension of signal.
By default, the
brainperm() function produces the cluster-mass test, but you can choose the TFCE with the argument
multcomp = "tfce" or the Troendle’s procedure
multcomp = "troendle".
permuco4brain uses the
future package to handle multi-cores computing.
Visit https://jaromilfrossard.github.io/permuco4brain or check the vignette:
permuco4brainin combination with
vignette("permuco4brain-with-eeguana", package = "permuco4brain")
You will find information how to extract the 3D array, the design data-frame and the graph from an
eeg_lst object of the
eeguana package. Check the
eeguana package for pre-processing EEG data within
permuco4brainwith signals stored in
vignette("download-example-cheval", package = "permuco4brain")
In this tutorial, you learn how to download EEG data from
zenodo and analyze them using
futureto run the TFCE:
vignette("tfce", package = "permuco4brain")
ggplot2to produce graphical representation of the results for publication:
vignette("figure-ggplot2", package = "permuco4brain")
In this tutorial, you find 3 different types of plot that present the results of a cluster-mass test or TFCE. All of them use the
ggplot2 package and may easily be customized for publication.