pseudobulk: Pseudobulk Seurat objects at whole sample or celltype level

In FerrenaAlexander/FerrenaSCRNAseq: Package for QC, processing and analysis of scRNAseq data

Pseudobulk Seurat objects at whole sample or celltype level

Description

Pseudobulking is performed adding up gene expression values for each cell, for either cell types or whole sample.

Usage

pseudobulk(obj, grouping_colname_in_md, metadata, rawh5_path, assay, slot)

Arguments

obj	seurat object, or a matrix
grouping_colname_in_md	optional, a string, the column name of [e-mail] (if obj is a seurat object) or metadata (if using matrix and metadata input) to use as "cell types" or any other grouping for pseudobulking at group level. if not provided, pseudobulk the entire matrix. default, not used.
metadata	data.frame with cell metadata, similar to [e-mail]. pass this only if
rawh5_path	optional, a string, the path to a rawH5 file, if provided will use the raw matrix subsetted by cells in sobj; if not will just pseudobulk the seurat object. useful if some filtering was applied to seurat object but you want to pseudobulk the whole matrix without that filtering, but with only using cells in seurat object. Default is not to use this.
assay	optional, a string, the name of the Seurat object assay to pull matrix from if rawh5_path is not provided. Default is "RNA" assay
slot	optional, a string, the name of the Seurat object slot within the designated object assay to pull matrix from if rawh5_path is not provided. Default is "counts" slot

Value

a data.frame. if grouping_colname_in_md is provided, each celltype will have a pseudobulked column, if not the data.frame will just be one column for the whole sample matrix.

FerrenaAlexander/FerrenaSCRNAseq documentation built on March 10, 2023, 9:31 a.m.