Legacy compare function (deprecated) — compare

For each peptide this function carries out the selected tests to determine peptides that are differentially abundant in the two experiments specified. Before tests are performed the technical replicates are merged and lowest observed value replacement for each missing biological replicate is done. All comparisins are performed as `treatment / control`

Usage

compare_legacy(
  df,
  iters = 1000,
  treatment = NA,
  t_seconds = NA,
  control = NA,
  c_seconds = NA,
  tests = c("bootstrap_t")
)

Arguments

df: dataframe. Typically from `import_data()`
iters: number of iterations to perform for iterative tests
treatment: name of the experimental treatment to use as the `treatment` condition
t_seconds: time point of the `treatment` condition to use
control: name of the experimental treatment to use as the `control` condition
c_seconds: time point of the `control` condition to use
tests: character vector of tests to use, one or more of: `norm_quantile`, `bootstrap_t`, `wilcoxon`, `kruskal-wallis`, `rank_product`

Value

dataframe with original and replaced quantification values, natural fold change, biological replicates and p-value / fdr for each