Identify_ConservedMarkers: Identify orthologs marker genes for two species

In CACIMAR: Cross-Species Analysis of Cell Identities, Markers and Regulations

Identify orthologs marker genes for two species

Description

Identify orthologs marker genes for two species based on orthologs database

Usage

Identify_ConservedMarkers(
  OrthG,
  Species1_Marker_table,
  Species2_Marker_table,
  Species_name1,
  Species_name2,
  match_cell_name = NULL
)

Arguments

OrthG	ortholog genes database
Species1_Marker_table	data.frame of species 1, first column should be gene name, second column should be Clusters corresponding to marker gene
Species2_Marker_table	data.frame of species 2, first column should be gene name, second column should be Clusters corresponding to marker gene of marker genes.
Species_name1	character, indicating the species names of Species1_Marker_table.
Species_name2	character, indicating the species names of Species2_Marker_table
match_cell_name	characters contained in both cell names to match similar cell types

Value

Data frame of conserved markers

Examples

load(system.file("extdata", "CellMarkers.rda", package = "CACIMAR"))
o1 <- Identify_ConservedMarkers(OrthG_Mm_Zf,Mm_marker_cell_type,
Zf_marker_cell_type,Species_name1 = 'mm',Species_name2 = 'zf')
o2 <- Identify_ConservedMarkers(OrthG_Zf_Ch,Ch_marker_cell_type,
Zf_marker_cell_type,Species_name1 = 'ch',Species_name2 = 'zf')

CACIMAR documentation built on May 18, 2022, 9:07 a.m.