Description
I am now doing analysis using ParetoTI, and this is a question about the result enrich_set.
In the step’ Find genes and gene sets enriched near vertices’, I generate the enrich_set and enrich_gene for each archetype. In the conclusion, I find out several columns describing relative properties of the genes, but I cannot understand the meaning of some of them. The median_diff, mean_diff, top_bin_mean, and especially the sample_count are those I cannot understand. The sample count is not about the number of all the cells either the enriched cells generated by bin_cells_by_arch, I am not sure what it means.
The code I write is about (just like the example):
activ = measure_activity(data,
which = "BP", return_as_matrix = F,
taxonomy_id = 9606,
keys=rownames(data),
keytype = "SYMBOL",
lower = 50, upper = 2000,
aucell_options = list(aucMaxRank = nrow(data) * 0.1,
binary = F, nCores = 2,
plotStats = TRUE))
data_attr = merge_arch_dist(arc_data = arc_data, data = data,
feature_data = as.matrix(data),
colData = activ,
dist_metric = c("euclidean", "arch_weights")[1],
colData_id = "cells" , rank = F)
enriched_genes = find_decreasing_wilcox(data_attr$data, data_attr$arc_col,
features = data_attr$features_col,
bin_prop = 0.1, method = "BioQC",
)
enriched_sets = find_decreasing_wilcox(data_attr$data, data_attr$arc_col,
features = data_attr$colData_col,
bin_prop = 0.1,method = "BioQC")