Identify marker features for each phenotype

Source: R/get_trait_markers.R

Identify marker features for a set of phenotypes by taking the intersection between the top n_features in two assays.

get_phenotype_markers(
  seurat,
  terms = NULL,
  assay1 = "MAGMA",
  assay1_slot = "scale.data",
  assay2 = "specificity",
  assay2_slot = "counts",
  n_features = 100
)

Arguments

seurat

Seurat object.
terms

A list of substrings to search for in column names.
assay1

First assay name.
assay1_slot

Slot to use from assay1.
assay2

Second assay name.
assay2_slot

Slot to use from assay2.
n_features

Number of features to select per assay.