scWGNA.compare: Runs a comparative scWGCNA analysis

In CFeregrino/scWGCNA: WGCNA Analyses on Single-cell Data

Runs a comparative scWGCNA analysis

Description

This function runs a WGCNA analysis adapted for single cells. Based on single-cell or pseudocell data.

Usage

scWGNA.compare(
  scWGCNA.data,
  test.list,
  test.names,
  ortho = NULL,
  ortho.sp = NULL,
  is.pseudocell = T,
  ...
)

Arguments

scWGCNA.data	The WGCNA data to use as reference for comparative analysis. Output from run.scWGCNA
test.list	List of Seurat objects. The samples to test conservation in. If data is calculated on pseudocells, these should also be pseudocell objects
test.names	Vector of strings. Contains the names for each of the samples in test.
ortho	Data frame. If the test objects and the reference data have different feature names, a data frame should be provided. Only listing 1-to-1 orthologous genes. The species of the reference MUST always be column no. 1
ortho.sp	Vector numeric. Indicating to which species in ortho each test sample belongs to.
is.pseudocell	Logic. Is the analysis based on pseudocells?
...	Further parameters, passed to WGCNA::modulePreservation

Value

It returns a new object, main result of WGCNA::modulePreservation

Examples

# A pre-calculated WGCNA data list
class(MmLimbE155.scWGCNA)
Mm.scW = MmLimbE155.scWGCNA

# A Seurat object with chicken limb cells
my.small_GgLimbHH29

# We calculate pseudocells for this object
Gg.ps=calculate.pseudocells(my.small_GgLimbHH29, dims = 1:10)

# Our Seurat objects contain gene names equivalencies in the misc slot.
# We use them to biuld a table of orthologous genes
my.ortho = merge(my.small_MmLimbE155@misc$gnames,my.small_GgLimbHH29@misc$gnames, by = "Gene.name")
my.ortho=my.ortho[,2:3]

# Comparative tests
MmvGg = scWGNA.compare(Mm.scW, test.list=list(Gg.ps), test.names="Gg", ortho=my.ortho, ortho.sp=2)

CFeregrino/scWGCNA documentation built on Nov. 21, 2022, 2:31 a.m.