Parse pairedGSEA results into geneSetSimplifyR input

Converts pairedGSEA::paired_ora() output into the two inputs geneSetSimplifyR() needs: geneSetsList and geneSetsDF (with source, pathway, enrichment_score). Each of the three blocks (expression, splicing, paired) is filtered by its own padj cutoff and added as a separate source. Pathways passing multiple cutoffs appear once per source.

Usage

parsePairedGSEA(
  oraResult,
  geneSets,
  cutoff_exp = 0.05,
  cutoff_splicing = 0.05,
  cutoff_paired = 0.05
)

Arguments

oraResult

Data frame from pairedGSEA::paired_ora(). Needs a pathway column plus padj_<block> and enrichment_score_<block> columns for each enabled block.

geneSets

Named list of gene-set memberships (the same one passed to pairedGSEA::paired_ora()).

cutoff_exp

padj cutoff for the expression block, or NULL to skip using expression. Default 0.05.

cutoff_splicing

padj cutoff for the splicing block, or NULL to skip using splicing. Default 0.05.

cutoff_paired

padj cutoff for the paired block, or NULL to skip it. Default 0.05.

Value

A list with:

geneSetsList

geneSets filtered to pathways passing at least one cutoff.

geneSetsDF

Long-format data frame: source, pathway, enrichment_score, padj and pval (when oraResult has pval_<block> columns). One row per (pathway, source).

Examples

# A small table in the format of pairedGSEA::paired_ora() output
pathways <- names(exampleGeneSets)[1:60]
oraResult <- data.frame(
  pathway = pathways,
  padj_expression = rep(c(0.01, 0.2), 30),
  enrichment_score_expression = seq(-2, 2, length.out = 60),
  padj_splicing = rep(c(0.2, 0.01, 0.01), 20),
  enrichment_score_splicing = seq(2, -2, length.out = 60),
  padj_paired = 1,
  enrichment_score_paired = 0
)
parsed <- parsePairedGSEA(
  oraResult       = oraResult,
  geneSets        = exampleGeneSets,
  cutoff_exp      = 0.05,
  cutoff_splicing = 0.05,
  cutoff_paired   = NULL
)
table(parsed$geneSetsDF$source)
#> 
#> expression   splicing 
#>         30         40 
gss <- geneSetSimplifyR(
  geneSetsList = parsed$geneSetsList,
  geneSetsDF   = parsed$geneSetsDF,
  resolution   = 1.1,
  verbose      = FALSE
)