pARI {pARI} | R Documentation |
Permutation-based All-Resolutions Inference
Description
The main function for All-Resolutions Inference (ARI) method based on critical vectors constructed
using the p-values permutation distribution. The function computes simultaneous lower bounds for the number of true discoveries
for each set of hypotheses specified in ix
controlling family-wise error rate.
Usage
pARI(X= NULL, ix, alpha = 0.05, family = "simes", delta = 0, B = 1000, pvalues = NULL,
test.type = "one_sample", complete = FALSE, clusters = FALSE, iterative = FALSE,
approx = TRUE, ncomb = 100, step.down = FALSE, max.step = 10, ...)
Arguments
X |
data matrix where rows represent the |
ix |
numeric vector which expresses the set of hypotheses of interest. It can be a vector with length equals |
alpha |
numeric value in '[0,1]'. It expresses the alpha level to control the family-wise error rate. |
family |
string character. Choose a family of confidence envelopes to compute the critical vector
from |
delta |
numeric value. It expresses the delta value, please see the references. Default to 0. |
B |
numeric value. Number of permutations, default to 1000. |
pvalues |
matrix of pvalues with dimensions |
test.type |
character string. Choose a type of tests among |
complete |
Boolean value. If |
clusters |
Boolean value. If |
iterative |
Boolean value. If |
approx |
Boolean value. Default @TRUE. If you are treating high dimensional data, we suggest to put |
ncomb |
Numeric value. If |
step.down |
Boolean value. Default @FALSE If you want to compute the lambda calibration parameter using the step-down approach put |
max.step |
Numeric value. Default to 10. Maximum number of steps for the step down approach, so useful when |
... |
Futher parameters. |
Value
by default returns a list with the following objects: discoveries
: lower bound for the number of true discoveries in the set selected, ix
: selected variables. If complete = TRUE
the raw pvalues
and cv
critical vector are returned.
Author(s)
Angela Andreella
References
For the general framework of All-Resolutions Inference see:
Goeman, Jelle J., and Aldo Solari. "Multiple testing for exploratory research." Statistical Science 26.4 (2011): 584-597.
For permutation-based All-Resolutions Inference see:
Andreella, Angela, et al. "Permutation-based true discovery proportions for fMRI cluster analysis." arXiv preprint arXiv:2012.00368 (2020).
See Also
The type of tests implemented: signTest
permTest
.
Examples
datas <- simulateData(pi0 = 0.8, m = 1000, n = 30, power = 0.9, rho = 0,seed = 123)
out <- pARI(X = datas, ix = c(1:200),test.type = "one_sample")
out