get_intersecting_pathways: Extract the intersection of gene sets which are enriched in...

In scITD: Single-Cell Interpretable Tensor Decomposition

Extract the intersection of gene sets which are enriched in two or more cell types for a factor

Description

Extract the intersection of gene sets which are enriched in two or more cell types for a factor

Usage

get_intersecting_pathways(
  container,
  factor_select,
  these_ctypes_only,
  up_down,
  thresh = 0.05
)

Arguments

container	environment Project container that stores sub-containers for each cell type as well as results and plots from all analyses
factor_select	numeric The factor to investigate
these_ctypes_only	character A vector of cell types for which to get gene sets that are enriched in all of these and not in any other cell types
up_down	character Set to "up" to get the gene sets for the positive loading genes. Set to "down" to get the gene sets for the negative loadings genes.
thresh	numeric Pvalue significance threshold for selecting enriched sets (default=0.05)

Value

A vector of the intersection of pathways that are significantly enriched in two or more cell types for a factor.

scITD documentation built on Sept. 8, 2023, 5:11 p.m.