R: select_top

select_top_markers {SCOPRO}

R Documentation

select_top_markers

Description

For each stage in selected_stages, starting from the markers given by markers_cluster_seurat function of the package CIARA, only the markers with a median above threshold in the stage and below threshold in all the other stages are kept.

Usage

select_top_markers(
  selected_stages,
  cluster_vivo,
  norm_vivo,
  markers_small,
  max_number = 100,
  threshold = 0.1
)

Arguments

`selected_stages`	Character vector with the name of the selected in vivo stages
`cluster_vivo`	cluster for in vivo dataset
`norm_vivo`	Norm count matrix (n_genes X n_cells) for in vivo dataset
`markers_small`	Output given by the function markers_cluster_seurat of the package CIARA
`max_number`	Numeric value. Maximum number of top markers to consider for each stage in selected_stages
`threshold`	Numeric value.

Value

A list with two elements:

`marker_all`	Vector with the union of all the top_number markers for each stage in selected_stages
`marker_stages`	List with length equal to number of stages in selected_stages . Each element contains the top_number markers for a given stage in selected_stages

Author(s)