scWGCNA: scWGCNA

In milescsmith/scWGCNA: scWGCNA

Description

Perform Weighted Gene Co-expression Network Analysis on scRNAseq data in a Seurat object

Usage

scWGCNA(object, min.module.size = 50, minFraction = 0.25,
  filter_mito_ribo_genes = FALSE, assay_use = NULL, slot_use = NULL,
  merge_similar_modules = FALSE, merge_similarity_threshold = 0.25)

Arguments

object	Processed scRNAseq object
min.module.size	Minimum number of genes needed to form an expression module. Default: 50.
minFraction	When determining genes to keep, what is the minimum fraction of samples a gene must be detected in before being remove? Default: 0.25
filter_mito_ribo_genes	Should mitochondrial and ribosomal genes be removed? Default: FALSE
assay_use	Instead of using expression data from the obj@data slot, use data stored in the obj@assay slot
slot_use	Assay data slot to use (i.e. "raw.data", "data", or "scale.data"). Default: 'data'
merge_similar_modules	Should similar modules be merged? Default: FALSE
merge_similarity_threshold	Dissimilarity (i.e., 1-correlation) cutoff used to determine if modules should be merged. Default: 0.25

milescsmith/scWGCNA documentation built on May 28, 2019, 12:23 p.m.