Test all treatments against a control group

Runs cr_test() pairwise for every treatment versus the control and adjusts p-values across comparisons.

Usage

cr_test_all(
  experiment,
  channel,
  control_group,
  tests = "mann_whitney",
  p_adjust = "BH",
  level = c("replicate", "cell", "both")
)

Arguments

experiment

A cr_experiment.

channel

Channel name.

control_group

Control group.

tests

Tests to run (see cr_test()). First one is used for the summary p-value.

p_adjust

P-value adjustment method (see stats::p.adjust).

level

"cell" or "replicate" or "both".

Value

A list of cr_result objects plus an attribute summary holding a single overview tibble.

Examples

# \donttest{
exp <- cr_example_experiment(seed = 1, n_cells_per_well = 20)
all_res <- cr_test_all(exp, channel = "marker_1",
                       control_group = "Untreated",
                       level = "replicate")
attr(all_res, "summary")
#> # A tibble: 5 × 6
#>   treatment       log2_fc    p_value cohens_d      p_adj interpretation
#>   <chr>             <dbl>      <dbl>    <dbl>      <dbl> <chr>         
#> 1 PosControl        3.40  0.00000154   2.12   0.00000466 strong        
#> 2 CompoundA_low     1.07  0.0000312    0.469  0.0000520  weak          
#> 3 CompoundA_high    3.05  0.00000186   2.08   0.00000466 strong        
#> 4 CompoundA_ScavX   0.495 0.00273      0.0445 0.00273    weak          
#> 5 CompoundA_ScavY   0.923 0.0000820    0.487  0.000102   weak          
# }