matchCellMarker2: Match Markers with cellMarker2 Dataset

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

Match Markers with cellMarker2 Dataset

Description

This function matches markers from the FindAllMarkers output with the cellMarker2 dataset, filtering by species and selecting the top genes based on their average log2 fold change and adjusted p-values.

Usage

matchCellMarker2(
  marker,
  n,
  spc,
  tissueClass = available_tissue_class(spc),
  tissueType = available_tissue_type(spc)
)

Arguments

marker	A data frame of markers obtained from the FindAllMarkers function, expected to contain columns such as avg_log2FC, p_val_adj, and gene.
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).

Value

A data frame containing matched markers from the cellMarker2 dataset, with additional columns indicating the number of matches and ordered symbols.

Examples

# Example usage:
# Match the top 50 differential genes from the pbmc.markers dataset with the Human
# species in the cellMarker2 dataset.
## Not run: 
library(easybio)
data(pbmc.markers)
matchCellMarker2(pbmc.markers, n = 50, spc = "Human")[]

## End(Not run)

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