Prepare enrichment data with common computed columns

Adds neg_log_fdr, direction, and significant columns to enrichment results. This is a shared helper used by plot functions and analyses.

Usage

prepare_enrichment_data(data, fdr_col = "FDR", fdr_threshold = 0.1)

Arguments

data

Data frame with NES and FDR columns

fdr_col

Name of FDR column (default: "FDR")

fdr_threshold

FDR threshold for significance (default: 0.1)

Value

Data frame with added neg_log_fdr, direction, significant columns

Examples

# Basic usage with default FDR column
df <- data.frame(NES = c(1.5, -1.2, 0.5, -0.3), FDR = c(0.01, 0.08, 0.05, 0.25))
result <- prepare_enrichment_data(df)
result$direction   # "Up", "Down", "Up", "Down"
#> [1] "Up"   "Down" "Up"   "Down"
result$significant # TRUE, TRUE, TRUE, FALSE
#> [1]  TRUE  TRUE  TRUE FALSE

# With custom FDR column name (e.g., from clusterProfiler)
df2 <- data.frame(NES = c(2.0, -1.5), p.adjust = c(0.02, 0.12))
result2 <- prepare_enrichment_data(df2, fdr_col = "p.adjust")

# With stricter FDR threshold
result3 <- prepare_enrichment_data(df, fdr_threshold = 0.05)
result3$significant # TRUE, FALSE, TRUE, FALSE
#> [1]  TRUE FALSE FALSE FALSE