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Log normalisation and PCA computation

lognormalize_and_pca.Rd

This function wrapps the default Seurat analysis of 1. data normalisation, 2. identification of HVGs, 3. scaling expression and computing PCA. If a list of Seurat objects is provided this is performed for each element in the list.

Usage

lognormalize_and_pca(seu, npcs = NULL, n_hvgs = 3000, ...)

# S3 method for list
lognormalize_and_pca(seu, npcs = NULL, n_hvgs = 3000, ...)

# S3 method for Seurat
lognormalize_and_pca(seu, npcs = NULL, n_hvgs = 3000, ...)

Arguments

seu

Seurat object or list of Seurat objects(required).

npcs

Number of Principal Components (PCs) to compute. If NULL, PCA analysis is skipped.

n_hvgs

Number of highly variable genes (HVGs) to compute. Only HVGs will be used as input to PCA.

...

Additional named parameters passed to Seurat functions.

Value

List of processed Seurat objects. If a single sample, returns a processed Seurat object instead of a list.

Author

C.A.Kapourani C.A.Kapourani@ed.ac.uk