Calculate per-feature temporal properties for each group from the mean of replicates at each time point.
Arguments
- se_obj_merged_list
A list of SummarizedExperiment objects created by
merge_replicates(), each containing the mean of replicates for each feature at each time point for one group.- threshold
A numeric value to determine whether a feature is "expressed" in samples. (default is NULL, meaning any non-NA value is considered expressed).
Value
A list of SummarizedExperiment objects, each corresponding to one group, with updated rowData containing the following columns: Feature, Group, Exp_threshold, T_exp (number of time points with values > Exp_threshold), T_total (total number of time points), P_trend (p-value from Bartels' test for randomness against a trend), Max_FC (maximum fold change across time points), Max_FC_time (difference between the time points at which maximum and minimum expression occur; positive if max occurs after min, negative otherwise), Exp_ratio (T_exp / T_total), Rho_time (Spearman correlation with time; positive = up trend), Peak_ratio (number of local maxima / T_total; 0 = no peaks detected), Log2_CV (log2(1 + CV) of expression across time points), AUC (area under the time-0-normalised curve from assay 2; NA if assay 2 is not available).
Examples
data(example_obj)
example_obj <- normalise_to_start(example_obj)
#> Normalising to group baseline at each feature's first non-NA time point.
example_obj_list <- split_groups(example_obj)
example_obj_merged_list <- merge_replicates(example_obj_list)
example_obj_merged_list <-
calc_feature_property(example_obj_merged_list, threshold = 0)