`r lifecycle::badge("deprecated")`
This function is deprecated because Rank Products requires ranking across
ALL peptides, not within single peptides. The per-peptide permutation
approach produces unreliable p-values.
Use `compare()` with `test = "rankprod"` instead, which properly uses the
RankProd package to rank across all peptides.
Usage
test_rankprod(control, treatment, n_perm = 1000, seed = NULL)
Arguments
- control
Numeric vector of control group values
- treatment
Numeric vector of treatment group values
- n_perm
Number of permutations for p-value estimation (default 1000)
- seed
Optional random seed for reproducibility
Value
A list with components:
- p_value_up
P-value for upregulation (treatment > control)
- p_value_down
P-value for downregulation (treatment < control)
- p_value
Combined two-sided p-value (minimum of up/down)
- rp_up
Rank product for upregulation
- rp_down
Rank product for downregulation
- method
"rankprod"
Examples
ctrl <- c(100, 120, 110, 105)
trt <- c(200, 220, 180, 210)
if (FALSE) { # \dontrun{
test_rankprod(ctrl, trt, n_perm = 100) # Deprecated
} # }
