da_Run: Run differential abundance analysis.

In NMikolajewicz/scMiko: scRNAseq analysis functions. Developed using Seurat framework.

Run differential abundance analysis.

Description

Run differential abundance analysis. Adapted Milo method in a wrapper.

Usage

da_Run(
  object,
  condition.group,
  sample.group = NA,
  design.groups = c(condition.group, sample.group),
  balance.samples = T,
  balance.size = NA,
  assay = DefaultAssay(object),
  reference.group = NULL,
  fdr.correction = F
)

Arguments

object	Seurat object
condition.group	Character specifying which metadata column to perform differential analysis on.
sample.group	Character specifying metadata column with replicate groupings. If not specified (Default), pseudoreplicates are generated (see scMiko::pseudoReplicates()).
design.groups	Character vector specifying model design. Default: c(condition.group, sample.group).
balance.samples	Numeric specifying target sample size when balancing samples. 'balance.size' argument for scMiko::balanceSamples.
assay	Character specifying which Seurat assay to use.
reference.group	Character specifying which condition.group is reference.
fdr.correction	Logical to perform FDR correction.

Value

list of results

Author(s)

Nicholas Mikolajewicz

NMikolajewicz/scMiko documentation built on June 28, 2023, 1:41 p.m.