Trim PTMsigDB pathways to shorter flanking sequences — trim_ptmsigdb

Trims all site IDs in PTMsigDB pathways to specified width. Use this when trimming your data with ptmsea_data_prep(trim_to=...) to ensure both sides match.

Usage

trim_ptmsigdb_pathways(pathways, trim_to = c("11", "13", "15"))

Arguments

pathways: Named list of pathways from fgsea::gmtPathways().
trim_to: Character. Target width: "11" (default), "13", or "15" (no trim).

Value

Named list of pathways with trimmed site IDs.

Examples

# Mock pathways
pathways <- list(
  PathwayA = c("AAAAAAASAAAAAAA-p", "BBBBBBBSBBBBBBB-p"),
  PathwayB = c("CCCCCCCSCCCCCCC-p")
)

# Trim to 11-mer
pathways_11 <- trim_ptmsigdb_pathways(pathways, trim_to = "11")