getPvalues: Gets p-values for Simulation Study

In neuroconductor-devel/pbj: Parametric Bootstrap Joint Testing Procedures for Neuroimaging

Description

Gets p-values for Simulation Study

Usage

getPvalues(pmap, betamap = NULL, kernel = "box", pfunc = function(x)
  10^(-abs(x)))

Arguments

pmap	A cluster-extent p-value map (nii, nii.gz, or Nifti object), where each cluster is labeled with its FWE adjusted cluster-extent p-value. (Required argument)
betamap	A known betamap (nii, nii.gz, or Nifti object) used in simulations to generate artificial signal in the imaging outcome. If NULL then power statistics are not reported.
kernel	What type of kernel to use for connected components. Defaults to "box".
pfunc	If pmap is transformed p-values then what function should be used to compute untransformed p-values. Uses pbj default, which stores p- values as -log10(p).

Value

Returns a list with the following values:

altp	If betamap is non-NULL then this returns a list the length of the number of connected components in betamap. Each list element gives the ordered p-values of clusters in pmap that have nonempty overlap with that cluster in betamap. The output is ordered by increasing size of connected components in betamap. NULL if betamap is NULL.
nullp	If betamap is non-NULL then these are the p-values for clusters in pmap that have empty intersection with betamap. Otherwise, this is a vector of p-values for all clusters in pmap.
clustsize	If betamap us non-NULL then this is the sizes of clusters in betamap in increasing order. NULL otherwise.
altinds	If betamap is non-NULL then this returns a list the length of the number of connected components in betamap. Each list element gives the indices of clusters indices in componentmap that overlap with the corresponding cluster in betamap. NULL otherwise.
nullinds	Vector of indices of components in component map that do not overlap with betamap.
componentmap	Nifti object giving connected components of pmap.

neuroconductor-devel/pbj documentation built on May 7, 2021, 7:53 p.m.