pseudobulk: pseudobulk

In ddiez/scmisc: Miscellaneus Tools for the Analysis of Single Cell Data

pseudobulk

Description

Generate pseudobulk counts of single cell data per cell population and sample name. Return a list of DGEList objects.

Usage

pseudobulk(
  x,
  split.by,
  group.by,
  samples = NULL,
  genes = NULL,
  sort_samples = TRUE,
  ...
)

## S3 method for class 'Seurat'
pseudobulk(
  x,
  split.by,
  group.by,
  samples = NULL,
  genes = NULL,
  assay = NULL,
  layers = "counts",
  sort_samples = TRUE,
  ...
)

Arguments

x	Seurat object.
split.by	Split single cell data using this column. Typically cell populations or clusters.
group.by	Aggregate counts from cells in each group. Typically sample names.
samples	A data.frame with sample information to include in slot "samples" in the DGEList object.
genes	A data.frame with gene information to include in slot "genes" in the DGEList object.
sort_samples	whetner to sort the columns of the pseudobulk samples based on the order in the samples data.frame.
assay	Seurat assay to use. Default: NULL (default assay).
layers	Seurat layers to use. Default: counts.

ddiez/scmisc documentation built on July 21, 2024, 11:35 a.m.