Statistics about literature curated ligand-receptor interactions
Source:R/intercell_curated.R
curated_ligrec_stats.Rd
Statistics about literature curated ligand-receptor interactions
Arguments
- ...
Passed to
curated_ligand_receptor_interactions
, determines the set of all curated L-R interactions which will be compared against each of the individual resources.
Value
A data frame with estimated counts of curated ligand-receptor interactions for each L-R resource.
Details
The data frame contains the total number of interactions, the number of interactions which overlap with the set of curated interactions (curated_overlap), the number of interactions with literature references from the given resource (literature) and the number of interactions which are curated by the given resource (curated_self). This latter we defined according to our best knowledge, in many cases it's not possible to distinguish curated interactions). All these numbers are also presented as a percent of the total. Importantly, here we consider interactions curated only if they've been curated in a cell-cell communication context.
Examples
clr <- curated_ligrec_stats()
clr
#> # A tibble: 19 × 8
#> resource total curated_over…¹ liter…² curat…³ curat…⁴ liter…⁵ curat…⁶
#> <chr> <int> <int> <int> <int> <dbl> <dbl> <dbl>
#> 1 CellPhoneDB 1475 1254 386 486 85.0 26.2 32.9
#> 2 Cellinker 3765 2315 3765 973 61.5 100 25.8
#> 3 CellTalkDB 3473 3421 3160 3160 98.5 91.0 91.0
#> 4 CellChatDB 1894 1210 569 569 63.9 30.0 30.0
#> 5 CellCall 999 779 0 0 78.0 0 0
#> 6 connectomeDB2020 2313 2313 2311 2311 100 99.9 99.9
#> 7 Guide2Pharma 670 588 295 295 87.8 44.0 44.0
#> 8 Baccin2019 1694 1414 1393 1393 83.5 82.2 82.2
#> 9 Kirouac2010 152 125 0 0 82.2 0 0
#> 10 Ramilowski2015 1946 1903 274 274 97.8 14.1 14.1
#> 11 scConnect 479 439 291 291 91.6 60.8 60.8
#> 12 talklr 2485 2364 274 273 95.1 11.0 11.0
#> 13 ICELLNET 738 736 735 735 99.7 99.6 99.6
#> 14 EMBRACE 1702 1615 0 0 94.9 0 0
#> 15 LRdb 3310 3136 2052 2052 94.7 62.0 62.0
#> 16 iTALK 2639 2491 0 0 94.4 0 0
#> 17 SignaLink 1797 242 1797 217 13.5 100 12.1
#> 18 HPMR 595 567 550 550 95.3 92.4 92.4
#> 19 Wojtowicz2020 438 163 0 0 37.2 0 0
#> # … with abbreviated variable names ¹curated_overlap, ²literature,
#> # ³curated_self, ⁴curated_overlap_pct, ⁵literature_pct, ⁶curated_self_pct