Get regional cross correlations and their p-values in a correlation list object.
get_correlations.Rd
This analysis will get regional cross correlations based on cell counts normalized by region volume.
Arguments
- e
experiment object
- by
(str) Attribute names to group by, e.g. c("sex", "group")
- values
(str) The respective values of the attributes entered for the
by
parameter to generate a specific analysis group, e.g.values = c("female", "AD").- channels
(str, channels = c("cfos", "eyfp", "colabel") The channels to process.
- p_adjust_method
(bool or str, default = "none") This parameter is fed into the p.adjust function. Options: c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none") Apply the named method to control for the inflated false discovery rate or family wise error rate (FWER). Set to FALSE or "none" to keep "raw" p values. See also
stats::p.adjust()
for the correction options.- alpha
(num, default = 0.05) The alpha level for significance applied AFTER p-adjustment.
- ontology
(str, default = "allen") Region ontology to use. options = "allen" or "unified"
- anatomical.order
(vec, c("Isocortex","OLF","HPF","CTXsp","CNU","TH","HY","MB","HB","CB")) The default super region acronym list that sorts all subregions in the dataset for grouped positioning in the correlation matrix. Supercedes
region_order
parameter.- region_order
(list, default = NULL) optional list with the first element named "acronym" supplying a vector as region acronyms and the second element named "order" supplying an vector of integers determining numerical order, e.g. 1, 1, 2, 2.
Value
e experiment object. The experiment object now has a named correlation_list
object stored in it.
The name of the correlation object is the concatenation of the variable values separated by a "_".
This name allows for unambiguous identification of different analysis subgroups in the future.