Prepare ranked lists for GSEA analysis

Creates named numeric vectors suitable for clusterProfiler::GSEA from phosphoproteomics data with multiple contrasts. This is a general-purpose function that works with any GSEA analysis (Kinase Library, motif enrichment, etc.). For PTMsigDB-specific preparation with trimming and "-p" suffix, see ptmsea_data_prep.

Usage

prepare_gsea_ranks(
  data,
  stat_col,
  seq_col = "SequenceWindow",
  contrast_col = "contrast",
  to_uppercase = TRUE,
  add_suffix = NULL
)

Arguments

data

Data frame with phosphosite data containing statistics per contrast

stat_col

Character. Column name for ranking statistic (e.g., "statistic.site" for DPA or "tstatistic_I" for DPU)

seq_col

Character. Column name for sequence windows. Default "SequenceWindow"

contrast_col

Character. Column name for contrasts. Default "contrast"

to_uppercase

Logical. Convert sequences to uppercase. Default TRUE

add_suffix

Character or NULL. Suffix to add to sequences (e.g., "-p" for PTMsigDB format). Default NULL (no suffix)

Value

Named list of named numeric vectors, one per contrast. Each vector contains statistics named by sequence, sorted in descending order.

Details

For each contrast, the function:

1. Filters to the specified contrast

2. Processes sequences (uppercase, trim whitespace)

3. Removes rows with NA statistics

4. Keeps first occurrence of duplicate sequences

5. Sorts by statistic (descending) for GSEA

See also

ptmsea_data_prep for PTMsigDB-specific preparation with trimming

Examples

# Example with mock data
data <- data.frame(
  contrast = rep(c("A_vs_B", "C_vs_D"), each = 5),
  SequenceWindow = c("AAASAAAA", "BBBSBBB", "CCCSCCCC", "DDDSDDDD", "EEESEEEE",
                     "AAASAAAA", "FFFSFFF", "GGGSGGGG", "HHHSHHHH", "IIISIII"),
  statistic.site = c(2.5, 1.8, -0.5, -1.2, 0.3, 1.9, 2.1, -0.8, 0.1, -1.5),
  stringsAsFactors = FALSE
)

# Prepare ranks for Kinase Library GSEA (no suffix needed)
ranks <- prepare_gsea_ranks(data, stat_col = "statistic.site")
names(ranks)  # contrast names
#> [1] "A_vs_B" "C_vs_D"
head(ranks[[1]])  # ranked sequences for first contrast
#> AAASAAAA  BBBSBBB EEESEEEE CCCSCCCC DDDSDDDD 
#>      2.5      1.8      0.3     -0.5     -1.2 

# Prepare ranks for PTMsigDB (with "-p" suffix)
ranks_ptm <- prepare_gsea_ranks(data, stat_col = "statistic.site", add_suffix = "-p")