easybio (version 1.1.1)

check_marker: Verify Markers for Specific Clusters Using matchCellMarker

Description

This function checks the markers for specified clusters returned by the matchCellMarker2 function. It allows users to filter by species, cluster, and to specify whether to consider cis or trans interactions.

Usage

check_marker(
  marker,
  n,
  spc,
  tissueClass = available_tissue_class(spc),
  tissueType = available_tissue_type(spc),
  cl = c(),
  topcellN = 2,
  cis = FALSE
)

Value

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

Arguments

marker

A data frame of markers obtained from Seurat::FindAllMarkers.

n

An integer specifying the top number of genes to match from the input markers.

spc

A character string specifying the species, which can be either 'Human' or 'Mouse'.

tissueClass

A character specifying the tissue classes, default available_tissue_class(spc).

tissueType

A character specifying the tissue types, default available_tissue_type(spc).

cl

An integer or vector of integers specifying the clusters to check.

topcellN

An integer specifying the number of top cells to check for each cluster.

cis

A logical value indicating whether to check marker directly from the top symbol of matchCellMarker2 or re-search marker for top cell in cellMarker2.

Examples

# Example usage:
# Check the top 50 markers for clusters 1, 4, and 7 in the Human species.
if (FALSE) {
library(easybio)
data(pbmc.markers)
check_marker(pbmc.markers, n = 50, spc = "Human", cl = c(1, 4, 7))
}