Comparing Uni-directional Signatures

This vignette demonstrates compare_omic_signatures() when every signature being compared is uni-directional: a single feature set, with no group_label contrast at all. See vignette("CompareSignatures") for the general bi-directional workflow, and vignette("CompareMixedDirection") for a list that mixes uni- and bi-directional signatures.

The example data

compare_unidirectional_example contains three simulated uni-directional signatures sharing a 100-gene universe. uni_x and uni_y share 5 of their 10 features each; uni_z shares nothing with either.

library(OmicSignature)

data(compare_unidirectional_example)

## direction_type per signature
sapply(compare_unidirectional_example, \(x) x$metadata$direction_type)
#>             uni_x             uni_y             uni_z 
#> "uni-directional" "uni-directional" "uni-directional"

Overlap: a flat comparison, with no level structure

Bi-directional signatures are compared level by level (level1_vs_level1, level2_vs_level2, …), since group_label gives each one two feature sets to pair up. Uni-directional signatures have no such pairing to make, so when every signature in both sig_list1 and sig_list2 is uni-directional, compare_omic_signatures() returns one flat comparison instead: comparisons directly holds jaccard, pvalue, and counts, and label_order is NULL.

uni_res <- compare_omic_signatures(
  sig_list1 = compare_unidirectional_example,
  method = "overlap",
  min_features = 3
)

names(uni_res$comparisons)
#> [1] "jaccard" "pvalue"  "counts"
uni_res$label_order
#> NULL

uni_res$comparisons$jaccard
#>           uni_x     uni_y uni_z
#> uni_x 1.0000000 0.3333333     0
#> uni_y 0.3333333 1.0000000     0
#> uni_z 0.0000000 0.0000000     1
uni_res$comparisons$counts
#>       uni_x uni_y uni_z
#> uni_x    10     5     0
#> uni_y     5    10     0
#> uni_z     0     0    10

KS and GSEA are not possible without a ranking

ks_rank, ks_score, and gsea need a two-group contrast to build a ranked vector to test against, which no uni-directional signature can provide. If none of sig_list2 is bi-directional with a difexp table, compare_omic_signatures() cannot construct a ranking side at all, and errors accordingly:

compare_omic_signatures(compare_unidirectional_example, method = "ks_rank")
#> Error in `.cos_check_ranking_capable()`:
#> ! No signatures in sig_list2 are bi-directional with a difexp table, required as the ranking side for method = 'ks_rank'.