Extract feature trends

Extract features with different segment trends from trendy segmented regression results summary

Usage

extract_segment_trends(trendy.summary)

Arguments

trendy.summary

A data frame, output of summarise_Trendy(), containing the segmented regression results for all features in all groups.

Value

A nested list of features grouped by their segment trend patterns within each group.

Examples

data("example")
example_obj <- normalise_to_start(example_obj)
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)
# no missing value in the example dataset, so imputation is not necessary
example_obj_merged_imp_list <- impute_groups(example_obj_merged_list)

# "untreated" group has only 3 time points, so Trendy analysis will not 
# be performed for this group
# example_res_list <- run_Trendy(example_obj_merged_imp_list, maxK = 1,
#     minNumInSeg = 2, meanCut = 0)
data("example_res_list")

plot_segments(example_obj_merged_imp_list, example_res_list,
    feature = c("Mctp1"))
#> Plotting segmented regression for group: IFNbeta

#> Plotting segmented regression for group: IFNgamma

#> Plotting segmented regression for group: LPS

plot_breakpoints(example_res_list)
#> Warning: number of columns of result is not a multiple of vector length (arg 9)
#> Warning: number of columns of result is not a multiple of vector length (arg 3)
#> Warning: number of columns of result is not a multiple of vector length (arg 5)

trendy_summary <- summarise_Trendy(example_res_list)
#> Warning: number of columns of result is not a multiple of vector length (arg 9)
#> Warning: number of columns of result is not a multiple of vector length (arg 3)
#> Warning: number of columns of result is not a multiple of vector length (arg 5)
trendy_list <- extract_segment_trends(trendy_summary)