CalculatePWProfiles: Calculate pathway enrichment profile

In BaderLab/Tempora: Pathway-based Trajectory Inference for Time-series Single Cell RNA-Seq Data

Description

Calculate cluster average gene expression profile and determine the pathway enrichment profile of each cluster

Usage

CalculatePWProfiles(
  object,
  gmt_path,
  method = "gsva",
  min.sz = 5,
  max.sz = 200,
  parallel.sz = 1
)

Arguments

object	A Tempora object containing a gene expression matrix and metadata (cluster identity and )
gmt_path	Local path to database of pathways or genesets organized as a .gmt file. Genesets files in GMT format can be downloaded at http://baderlab.org/GeneSets. Please ensure
method	Method used to estimate pathway enrichment profile per cluster. Can be "gsva", "ssgsea", "zscore" or "plage", default to "gsva". See ?gsva for more information.
min.sz	Minimum size of the genesets used in enrichment estimation, set to 5 genes by default.
max.sz	Maximum size of the genesets used in enrichment estimation, set to 200 genes by default.
parallel.sz	Type of cluster architecture when using snow. If 1, no parallelization will be used. If 0, all available cores will be used.

Value

An updated Tempora object containing the pathway enrichment profiles of each cluster, which can be accessed at [e-mail] CalculatePWProfiles

Examples

## Not run: tempora_data <- CalculatePWProfiles(tempora_data, gmt_path="~/Human_AllPathways_September_01_2019_symbol.gmt", parallel.sz = detectCores()-2)

BaderLab/Tempora documentation built on April 25, 2021, 2:10 p.m.