Skip to contents

Perform gene overrepresentation analysis and annotate biclusters.

annotate_biclustering.Rd

Wrapper function for `per_cluster_goa` and `annotate_by_goa`.

Usage

annotate_biclustering(
  obj,
  universe,
  org,
  set = "CellMarker",
  alpha = 0.05,
  min_size = 10,
  max_size = 500,
  verbose = TRUE,
  ...
)

# S4 method for caclust
annotate_biclustering(
  obj,
  universe,
  org,
  set = "CellMarker",
  alpha = 0.05,
  min_size = 10,
  max_size = 500,
  verbose = TRUE,
  ...
)

# S4 method for SingleCellExperiment
annotate_biclustering(
  obj,
  universe,
  org,
  set = "CellMarker",
  alpha = 0.05,
  min_size = 10,
  max_size = 500,
  verbose = TRUE,
  ...,
  caclust_meta_name = "caclust"
)

# S4 method for caclust
annotate_biclustering(
  obj,
  universe,
  org,
  set = "CellMarker",
  alpha = 0.05,
  min_size = 10,
  max_size = 500,
  verbose = TRUE,
  ...
)

Arguments

obj

Either a `caclust` or `SingleCellExperiment` object.

universe

All genes in data set.

org

Short name of the organism. "mm" for mouse, "hs" for human.

set

Name of the gene set. Currently only supports "CellMarker"

alpha

Adjusted p-value cutoff. Only results with padj < alpha will be used.

min_size

Min. number of genes in the gene set.

max_size

Max number of genes in the gene set. Set to Inf if you want to keep all genes.

verbose

Toggles verbosity of warnings.

...

Further arguments.

caclust_meta_name

Name under which the caclust object is stored in the metadata of the SingleCellExperiment object.

Value

An object of type `caclust` with annotated biclusters.

Details

`annotate_biclustering` performs per cluster GOA with a hypergeometric and annotates the biclustering results from CAbiNet.