do.fgsea: Runs GSEA on a pre-ranked list of differential expression...

In lianos/multiGSEA: A unified interface to a plethora of gene set enrichment analysis methods

Description

fgsea expects the pathways to be describes as a list of character vectors where the vectors are gene ids, and the names of the pre-ranked vector correspond to those IDs

Usage

do.fgsea(
  gsd,
  x,
  design,
  contrast = ncol(design),
  sampleSize = 101,
  eps = 1e-10,
  scoreType = c("std", "pos", "neg"),
  nproc = 0,
  gseaParam = 1,
  nPermSimple = 1000,
  absEps = NULL,
  use.fgsea.simple = FALSE,
  score.by = c("t", "logFC", "pval"),
  logFC = NULL,
  gs.idxs = as.list(gsd, active.only = TRUE, value = "x.idx"),
  ...
)

Arguments

gsd	The GeneSetDb() for analysis
x	The expression object. This can be 1 column matrix if you are not running any analysis, and this function essentially is just a "pass through"
design	The design matrix for the experiment
contrast	The contrast you want to test and provide stats for. By default this tests the last column of the design matrix. If you want to test a custom contrast, this can be a contrast vector, which means that it should be as long as ncol(design) and it most-often sum to one. In the future, the user will be able to specify a range of coefficients over design to perform an ANOVA analysis, cf. Issue #11 (https://github.com/lianos/multiGSEA/issues/11).
...	arguments to pass down into calculateIndividualLogFC()

Details

Deafults fgsea functionality was changed to fgsea::fgseaMultilevel() in 1.13.2 and the default parameters here reflect that. If you want to use the original "fgseaSimple" you have to pass in use.fgsea.simple = TRUE in your multiGSEA() call.

minSize and maxSize are already set by the conform logic that was specified in the call to multiGSEA() via the min.gs.size and max.gs.size parameters.

This function is not meant to be called directly. It should only be called internally within multiGSEA().

Value

A data.table of fgsea results.

lianos/multiGSEA documentation built on Nov. 17, 2020, 1:26 p.m.