This function performs a permutation analysis to compare the region pairwise correlation coefficients between two different analysis groups.
correlation_diff_permutation.Rd
The data from two different analysis groups are compared by specifying the
correlation_list_name_1
and correlation_list_name_2
parameters. Note that both of these analysis groups must have the same
number of channels to compare. The functions get_correlations()
needs to have been run for each of these analysis groups prior to
running this function. The test statistics used is the pearson values of those in correlation_list_name_2 subtracted from corresponding Pearson values in correlation_list_name_1.
Usage
correlation_diff_permutation(
e,
correlation_list_name_1,
correlation_list_name_2,
channels = c("cfos", "eyfp", "colabel"),
n_shuffle = 1000,
seed = 5,
p_adjust_method = "BH",
alpha = 0.05,
...
)
Arguments
- e
experiment object
- correlation_list_name_1
(str) The name of the correlation list object used as the first group for comparison.
- correlation_list_name_2
(str) The name of the correlation list object used as the second group for comparison.
- channels
(str, default = c("cfos", "eyfp", "colabel")) The channels to process.
- n_shuffle
(int, default = 1000) The number of permutation shuffles.
- seed
(int, default = 5) Random seed for future replication.
- p_adjust_method
(bool or str, default = "BH") Benjamini-Hochberg method is recommended. Apply the named method to control for the inflated false discovery rate or FWER. Set to FALSE or "none" to keep "raw" p values. See also
stats::p.adjust()
for the correction options.- alpha
(float, default = 0.05) The alpha cutoff for significance between region pairwise correlation differences
Value
e experiment object. The experiment object now has a list called permutation_p_matrix
stored in it. Elements of this permutation_p_matrix
list are
the outputs of different permutation comparison analyses. These elements are named by the groups that were compared.