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Milo differential abundance wrapper

Source: R/RunMilo.R
RunMilo.Rd

Method-specific implementation used by RunProportionTest when proportion_method = "milo". The function always returns a group-level summary and additionally stores a neighborhood-level result list under neighborhood_results.

Usage

RunMilo(
  srt,
  group.by,
  split.by,
  sample.by,
  comparison = NULL,
  milo_k = 20L,
  milo_d = 30L,
  n_bootstrap = 500,
  seed = 11,
  verbose = TRUE
)

Arguments

srt

A Seurat object.

group.by

Name of one or more meta.data columns to group (color) cells by.

split.by

Metadata column that identifies the condition groups to compare. For sample-level methods, if split.by is omitted and sample.by is provided, sample.by is treated as the condition column and virtual samples are created within each condition.

sample.by

Metadata column that identifies biological samples. For "milo", "sccoda", and "propeller", when sample.by is omitted or identical to split.by, virtual samples are created within each split.by group for convenience.

comparison

Optional: specify comparisons to perform.

milo_k

Number of nearest neighbors used for Milo graph building.

milo_d

Number of dimensions used by Milo.

n_bootstrap

Number of bootstrap iterations used by the group-level summary.

seed

Random seed.

verbose

Whether to print the message. Default is TRUE.

Value

A method result bundle used internally by RunProportionTest.