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