Impute missing values in raw intensity using low-percentile sampling or geometric mean — impute_low1pct_or_median

Missing values within each condition are imputed either from the low-intensity distribution or via geometric mean when the majority of values are missing.

Usage

impute_low1pct_or_median_raw(
  df,
  id_col = "Protein.Ids",
  sample_col = "sample",
  value_col = "raw_value",
  condition_col = "condition",
  low_prob = 0.01,
  return_log2 = FALSE,
  seed = 1
)

Arguments

df: Long-format data.frame containing raw intensities.
id_col: Protein ID column.
sample_col: Sample name column.
value_col: Value column for raw intensity.
condition_col: Condition or group column.
low_prob: Low percentile used for imputation (default 0.01).
return_log2: Return log2 values instead of raw (default FALSE).
seed: Random seed.

Value

Long-format data.frame with imputed values.