get_marker: Retrieve Markers for Specific Cells from cellMarker2

In easybio: Comprehensive Single-Cell Annotation and Transcriptomic Analysis Toolkit

Retrieve Markers for Specific Cells from cellMarker2

Description

This function extracts a list of markers for one or more cell types from the cellMarker2 dataset. It allows filtering by species, cell type, the number of markers to retrieve, and a minimum count threshold for marker occurrences.

Usage

get_marker(
  spc,
  cell = character(),
  tissueClass = available_tissue_class(spc),
  tissueType = available_tissue_type(spc),
  number = 5,
  min.count = 1
)

Arguments

spc	A character string specifying the species, which can be either 'Human' or 'Mouse'.
cell	A character vector of cell types for which to retrieve markers.
tissueClass	A character specifying the tissue classes, default available_tissue_class(spc).
tissueType	A character specifying the tissue types, default available_tissue_type(spc).
number	An integer specifying the number of top markers to return for each cell type.
min.count	An integer representing the minimum number of times a marker must have been reported to be included in the results.

Value

A named list where each name corresponds to a cell type and each element is a vector of marker names.

Examples

# Example usage:
# Retrieve the top 5 markers for 'Macrophage' and 'Monocyte' cell types in humans,
# with a minimum count of 1.
library(easybio)
markers <- get_marker(spc = "Human", cell = c("Macrophage", "Monocyte"))
print(markers)

easybio documentation built on April 12, 2025, 1:59 a.m.