pARIgene: Permutation-based All-Resolutions Inference for Gene...

In angeella/ARIpermutation: Permutation-Based All-Resolutions Inference Method

Permutation-based All-Resolutions Inference for Gene Expression Data

Description

This function computes the lower bound for the number of true discoveries within each cluster (pathways) of Gene Expression Data.

Usage

pARIgene(X= NULL, pathways, alpha = 0.05, family = "simes", delta = 0, 
B = 1000, test.type = "one_sample", complete = FALSE, iterative = FALSE, 
approx = TRUE, ncomb = 100, step.down = FALSE, max.step = 10, ...)

Arguments

X	data matrix where rows represent the m variables and columns the n observations.
pathways	list of pathways where names indicates the name of the pathway.
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 "simes", "aorc", "beta" and "higher.criticism".#' @param alpha alpha level.
delta	numeric value. It expresses the delta value, please see the references. Default to 0.
B	numeric value. Number of permutations, default to 1000.
test.type	character string. Choose a type of tests among "one_sample", i.e., one-sample t-test, or "two_samples", i.e., two-samples t-tests. Default "one_sample".
complete	Boolean value. If TRUE the sets of critical vectors and the raw pvalues are returned. Default @FALSE.
iterative	Boolean value. If iterative = TRUE, the iterative method for improvement of confidence envelopes is applied. Default @FALSE.
approx	Boolean value. Default @TRUE. If you are treating high dimensional data, we suggest to put approx = TRUE to speed up the computation time.
ncomb	Numeric value. If approx = TRUE, you must decide how many random subcollections (level of approximation) considered.
step.down	Boolean value. Default @FALSE If you want to compute the lambda calibration parameter using the step-down approach put TRUE.
max.step	Numeric value. Default to 10. Maximum number of steps for the step down approach, so useful when step.down = TRUE.
...	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. I f 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.

angeella/ARIpermutation documentation built on Aug. 24, 2023, 3:36 p.m.