AUCell

Calculates regulatory activities using AUCell.

Usage

run_aucell(
  mat,
  network,
  .source = source,
  .target = target,
  aucMaxRank = ceiling(0.05 * nrow(rankings)),
  nproc = availableCores(),
  seed = 42,
  minsize = 5
)

Arguments

mat

Matrix to evaluate (e.g. expression matrix). Target nodes in rows and conditions in columns. rownames(mat) must have at least one intersection with the elements in network .target column.

network

Tibble or dataframe with edges and it's associated metadata.

.source

Column with source nodes.

.target

Column with target nodes.

aucMaxRank

Threshold to calculate the AUC.

nproc

Number of cores to use for computation.

seed

A single value, interpreted as an integer, or NULL for random number generation.

minsize

Integer indicating the minimum number of targets per source.

Details

AUCell (Aibar et al., 2017) uses the Area Under the Curve (AUC) to calculate whether a set of targets is enriched within the molecular readouts of each sample. To do so, AUCell first ranks the molecular features of each sample from highest to lowest value, resolving ties randomly. Then, an AUC can be calculated using by default the top 5% molecular features in the ranking. Therefore, this metric, aucell, represents the proportion of abundant molecular features in the target set, and their relative abundance value compared to the other features within the sample.

Aibar S. et al. (2017) Scenic: single-cell regulatory network inference and clustering. Nat. Methods, 14, 1083–1086.

See also

Other decoupleR statistics: decouple(), run_fgsea(), run_gsva(), run_mdt(), run_mlm(), run_ora(), run_udt(), run_ulm(), run_viper(), run_wmean(), run_wsum()

Examples

inputs_dir <- system.file("testdata", "inputs", package = "decoupleR")

mat <- readRDS(file.path(inputs_dir, "mat.rds"))
net <- readRDS(file.path(inputs_dir, "net.rds"))

run_aucell(mat, net, minsize=0, nproc=1, aucMaxRank=3)
#> # A tibble: 72 × 4
#>    statistic source condition score
#>    <chr>     <chr>  <chr>     <dbl>
#>  1 aucell    T1     S01       0.667
#>  2 aucell    T1     S02       0.667
#>  3 aucell    T1     S03       0.667
#>  4 aucell    T1     S04       1    
#>  5 aucell    T1     S05       0.333
#>  6 aucell    T1     S06       0.333
#>  7 aucell    T1     S07       1    
#>  8 aucell    T1     S08       1    
#>  9 aucell    T1     S09       1    
#> 10 aucell    T1     S10       1    
#> # ℹ 62 more rows