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Run GSEA for Phosphorylation Data

Source: R/enrichment.R
runGSEAforPhospho.Rd

runGSEAforPhospho performs Gene Set Enrichment Analysis (GSEA) for phosphorylation data.

Usage

runGSEAforPhospho(
  geneStat,
  ptmSetDb,
  nPerm,
  weight = 1,
  correl.type = c("rank", "symm.rank", "z.score"),
  statistic = c("Kolmogorov-Smirnov", "area.under.RES"),
  min.overlap = 5
)

Arguments

geneStat

A data frame containing gene statistics, with gene names as row names and a column named 'stat' for the statistics.

ptmSetDb

A data frame of post-translational modification (PTM) signature sets.

nPerm

A numeric value specifying the number of permutations for the null distribution.

weight

A numeric value for the weight parameter in the GSEA algorithm. If weight == 0 then the test statistics do not matter. Default is 1.

correl.type

A character string specifying the correlation type. Options are "rank", "symm.rank", and "z.score". Default is "rank".

statistic

A character string specifying the statistic to be used. Options are "Kolmogorov-Smirnov" and "area.under.RES". Default is "Kolmogorov-Smirnov".

min.overlap

A numeric specifying the minimum overlap required between gene sets and the input data. Default is 5.

Value

A tibble with enrichment scores and associated statistics for each PTM set.

Details

This function runs GSEA on phosphorylation data to identify enriched PTM sets. It calculates enrichment scores and p-values for each set, normalizes the scores, and adjusts p-values for multiple testing.