omicsTools Workflow

This example runs a feature table through validation, preprocessing, group comparison, and report export.

library(omicsTools)
data <- data.frame(
  sample_id = paste0("S", 1:6),
  group = rep(c("control", "case"), each = 3),
  feature_a = c(1, 2, 3, 2, 4, 6),
  feature_b = c(3, 4, 2, 4, 2, 3)
)
result <- process_omics_data(
  data, group_col = "group", reference = "control", comparison = "case"
)
result$comparison

## # A tibble: 2 × 12
##   feature_id reference comparison n_reference n_comparison mean_reference
##   <chr>      <chr>     <chr>            <int>        <int>          <dbl>
## 1 feature_a  control   case                 3            3              2
## 2 feature_b  control   case                 3            3              3
## # ℹ 6 more variables: mean_comparison <dbl>, pseudocount <dbl>, log2FC <dbl>,
## #   p_value <dbl>, status <chr>, fdr <dbl>

export_omics_results(result, "results")

Created by Yaoxiang Li.