lognormalize_and_pca: Log normalisation and PCA computation

In andreaskapou/SeuratPipe: Packaging common Seurat analysis tasks

Log normalisation and PCA computation

Description

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 class 'list'
lognormalize_and_pca(seu, npcs = NULL, n_hvgs = 3000, ...)

## S3 method for class '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(s)

C.A.Kapourani [e-mail]

andreaskapou/SeuratPipe documentation built on Nov. 22, 2022, 4:16 p.m.