select_top_markers: select_top_markers

In SCOPRO: Score Projection Between in 'Vivo' and in 'Vitro' Datasets

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)

Gabriele Lubatti [e-mail]

See Also

https://CRAN.R-project.org/package=CIARA

SCOPRO documentation built on Aug. 23, 2022, 9:05 a.m.