Run differential abundance analysis.

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

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

Nicholas Mikolajewicz