TestSoftPowersConsensus: TestSoftPowersConsensus

In smorabit/hdWGCNA: hdWGCNA

TestSoftPowersConsensus

Description

Compute the scale-free topology model fit for different soft power thresholds separately for each input dataset

Usage

TestSoftPowersConsensus(
  seurat_obj,
  powers = c(seq(1, 10, by = 1), seq(12, 30, by = 2)),
  use_metacells = TRUE,
  networkType = "signed",
  corFnc = "bicor",
  setDatExpr = FALSE,
  group.by = NULL,
  group_name = NULL,
  multi.group.by = NULL,
  multi_groups = NULL,
  wgcna_name = NULL,
  ...
)

Arguments

seurat_obj	A Seurat object
powers	numeric vector specifying soft powers to test
use_metacells	logical flag for whether to use the metacell expression matrix
networkType	The type of network to use for network analysis. Options are "signed" (default), "unsigned", or "signed hybrid". This should be consistent with the network chosen for ConstructNetwork
corFnc	Correlation function for the gene-gene correlation adjacency matrix.
setDatExpr	logical flag indicating whether to run setDatExpr.
group.by	A string containing the name of a column in the Seurat object with cell groups (clusters, cell types, etc). If NULL (default), hdWGCNA uses the Seurat Idents as the group.
group_name	A string containing a group present in the provided group.by column or in the Seurat Idents. A character vector can be provided to select multiple groups at a time.
multi.group.by	A string containing the name of a column in the Seurat object with groups for consensus WGCNA (dataset, sample, condition, etc)
multi_groups	A character vecrtor containing the names of groups to select
...	additional parameters passed to SetDatExpr

Examples

# TestSoftPowers(pbmc)

smorabit/hdWGCNA documentation built on Oct. 23, 2024, 11:19 p.m.