calc_da: Calculate differential abundance of cell count labels using...

In rnabioco/scbp: Boilerplate functions for single cell rna-seq analysis

Calculate differential abundance of cell count labels using edgeR

Description

Calculate differential abundance of cell count labels using edgeR

Usage

calc_da(
  sobj,
  cluster_col = NULL,
  sample_col = NULL,
  condition_col = NULL,
  custom_design = NULL
)

Arguments

sobj	seurat object
cluster_col	cluster or cell type column in meta.data
sample_col	sample column in meta.data
condition_col	column in meta.data indicating condition, defaults to sample_col if not specified
custom_design	design matrix for testing, defaults to '~condition_col'

Details

See [Orchestraing Single Cell Analysis](https://osca.bioconductor.org/multi-sample-comparisons.html#differential-abundance)

rnabioco/scbp documentation built on July 7, 2023, 10:10 p.m.