Parse fgsea results into geneSetSimplifyR input

Converts fgsea::fgsea() output into the two inputs geneSetSimplifyR() needs: geneSetsList and geneSetsDF (with source, pathway, enrichment_score). To combine several fgsea runs into one multi-source analysis, call this function once per run with a distinct source label and rbind() the resulting geneSetsDFs.

Usage

parseFgsea(fgseaResult, geneSets, cutoff = 0.05, source = "fgsea")

Arguments

fgseaResult

Output of fgsea::fgsea() or fgsea::fora(). Must contain pathway and padj columns, and either NES (GSEA) or foldEnrichment (over-representation analysis, used as log2(foldEnrichment)).

geneSets

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

cutoff

padj threshold for filtering pathways. Default 0.05.

source

Label written to the source column of geneSetsDF. Use a distinct value per run when combining multiple analyses. Default "fgsea".

Value

A list with:

geneSetsList

geneSets filtered to pathways passing the cutoff.

geneSetsDF

Long-format data frame: source, pathway, enrichment_score (fgsea's NES), pval (when present) and padj. One row per pathway.

Examples

# A small table in the format of fgsea::fgsea() output
pathways <- names(exampleGeneSets)[1:60]
fgseaRes <- data.frame(
  pathway = pathways,
  pval = rep(c(0.001, 0.01, 0.3), 20),
  padj = rep(c(0.004, 0.03, 0.5), 20),
  NES = seq(-2.5, 2.5, length.out = 60)
)
parsed <- parseFgsea(
  fgseaResult = fgseaRes,
  geneSets    = exampleGeneSets,
  cutoff      = 0.05,
  source      = "treatmentA"
)
head(parsed$geneSetsDF)
#>       source                                   pathway enrichment_score  pval
#> 1 treatmentA GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_UP        -2.500000 0.001
#> 2 treatmentA                     FISCHER_DREAM_TARGETS        -2.415254 0.010
#> 3 treatmentA                       LEE_BMP2_TARGETS_DN        -2.245763 0.001
#> 4 treatmentA            VECCHI_GASTRIC_CANCER_EARLY_UP        -2.161017 0.010
#> 5 treatmentA    SOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_UP        -1.991525 0.001
#> 6 treatmentA           CAIRO_HEPATOBLASTOMA_CLASSES_UP        -1.906780 0.010
#>    padj
#> 1 0.004
#> 2 0.030
#> 3 0.004
#> 4 0.030
#> 5 0.004
#> 6 0.030
gss <- geneSetSimplifyR(
  geneSetsList = parsed$geneSetsList,
  geneSetsDF   = parsed$geneSetsDF,
  resolution   = 1.1,
  verbose      = FALSE
)