ModulePreservation: ModulePreservation

In smorabit/hdWGCNA: hdWGCNA

ModulePreservation

Description

Computes module preservation statistics in a query dataset for a given reference dataset

Usage

ModulePreservation(
  seurat_obj,
  seurat_ref,
  name,
  n_permutations = 500,
  parallel = FALSE,
  seed = 12345,
  gene_mapping = NULL,
  genome_ref_col = NULL,
  genome_query_col = NULL,
  return_raw = FALSE,
  wgcna_name = NULL,
  wgcna_name_ref = NULL,
  ...
)

Arguments

seurat_obj	A Seurat object
seurat_ref	A Seurat object serving as the reference for the module preservation analysis
name	The name to give the module preservation analysis.
n_permutations	Number of permutations for the module preservation test.
parallel	logical determining whether to run preservation analysis in parallel
seed	random seed for the permutation analysis.
gene_mapping	a dataframe containing gene name mappings between the query and the reference dataset. One column should have the gene name in the query dataset, and anotehr column should have the corresponding gene name in the reference dataset.
genome_ref_col	the column name containing the gene names for the reference dataset
genome_query_col	the column name containing the gene names for the query dataset
return_raw	if TRUE, returns the module preservation statistics, else returns seurat_obj with the stats added to the hdWGCNA experiment.
wgcna_name	The name of the hdWGCNA experiment in the seurat_obj@misc slot
wgcna_name_ref	The name of the hdWGCNA experiment in the seurat_ref@misc slot

Details

ModulePreservation performs a statistical test to assess the preservation of co-expression modules identified in one dataset in an independent dataset. This method is originally described by Langfelder et al. in the 2011 paper "Is My Network Module Preserved and Reproducible?". This method can be used to assess biological differences in networks, as well as technical differences / reproducibility across different batches.

smorabit/hdWGCNA documentation built on July 20, 2024, 8:58 p.m.