collapsePathwaysGeseca: Collapse list of enriched pathways to independent ones...

In ctlab/fgsea: Fast Gene Set Enrichment Analysis

Collapse list of enriched pathways to independent ones (GESECA version, highly experimental).

Description

Collapse list of enriched pathways to independent ones (GESECA version, highly experimental).

Usage

collapsePathwaysGeseca(
  gesecaRes,
  pathways,
  E,
  center = TRUE,
  scale = FALSE,
  eps = min(c(1e-50, gesecaRes$pval)),
  checkDepth = 10,
  nproc = 0,
  BPPARAM = NULL
)

Arguments

gesecaRes	Table with results of running geseca(), should be filtered by p-value, for example by selecting ones with padj < 0.01.
pathways	List of pathways, should contain all the pathways present in 'gesecaRes'.
E	expression matrix, the same as in 'geseca()'.
center	a logical value indicating whether the gene expression should be centered to have zero mean before the analysis takes place. The default is TRUE. The value is passed to scale.
scale	a logical value indicating whether the gene expression should be scaled to have unit variance before the analysis takes place. The default is FALSE. The value is passed to scale.
eps	eps prameter for internal gesecaMultilevel runs. Default: min(c(1e-50, gesecaRes$pval))
checkDepth	how much pathways to check against
nproc	If not equal to zero sets BPPARAM to use nproc workers (default = 0).
BPPARAM	Parallelization parameter used in bplapply.

ctlab/fgsea documentation built on Dec. 21, 2024, 1:55 p.m.