SCOPRO {SCOPRO}

SCOPRO

Description

The mean expression profile of marker_stages_filter genes is computed for each cluster in the in vivo and in vitro dataset. For a given cluster, a connectivity matrix is computed with number of rows and number of columns equal to the length of marker_stages_filter. Each entry (i,j) in the matrix can be 1 if the fold_change between gene i and gene j is above fold_change. Otherwise is 0. Finally the connectivity matrix of a given name_vivo stage and all the clusters in the in vitro dataset are compared. A gene i is considered to be conserved between name_vivo and an in vitro cluster if the jaccard index of the links of gene i is above threshold.

Usage

SCOPRO(
  norm_vitro,
  norm_vivo,
  cluster_vitro,
  cluster_vivo,
  name_vivo,
  marker_stages_filter,
  threshold = 0.1,
  number_link = 1,
  fold_change = 3,
  threshold_fold_change = 0.1,
  marker_stages,
  selected_stages
)

Arguments

norm_vitro

Norm count matrix (n_genes X n_cells) for in vitro dataset

norm_vivo

Norm count matrix (n_genes X n_cells) for in vivo dataset

cluster_vitro

cluster for in vitro dataset

cluster_vivo

cluster for in vivo dataset

name_vivo

name of the in vivo stage on which SCOPRO is run

marker_stages_filter

output from the function filter_in_vitro

threshold

Numeric value. For a given gene, the jaccard index between the links from the in vivo and in vitro datasets is computed. If the jaccard index is above threshold, then the gene is considered to be conserved between the two datasets.

number_link

Numeric value. For a given gene in the in vivo dataset with links above number_link, the jaccard index between the links from in vitro and in vivo dataset is computed.

fold_change

Numeric value. For a given gene, the fold change between all the other genes is computed. If fold change is above fold_change, then there is a link with weight 1 between the two genes.

threshold_fold_change

Numeric value. Above threshold the fold change between genes is computed. Below threshold the difference between genes is computed.

marker_stages

Second element of the list given as output by the function select_top_markers

selected_stages

In vivo stages for which the markers where computed with the function select_top_markers

Value

A list with five elements:

common_link

Vector with the names of the genes conserved between name_vivo and all the clusters in the vitro dataset

no_common_link

Vector with the names of the genes not conserved between name_vivo and the clusters in the vitro dataset

link_kept

List with the names of the genes conserved between name_vivo and each single cluster in the vitro dataset

link_no_kept

List with the names of the genes not conserved between name_vivo and each single cluster in the vitro dataset

final_score

Numeric value, given by the fraction of conserved markers of name_vivo and each single cluster in the in vitro dataset

Author(s)

Gabriele Lubatti [e-mail]

Examples

load(system.file("extdata", "norm_es_vitro_small.Rda", package = "SCOPRO"))
n_es= norm_es_vitro_small
load(system.file("extdata", "norm_vivo_small.Rda", package = "SCOPRO"))
n_v = norm_vivo_small
load(system.file("extdata", "cluster_es_vitro_small.Rda", package = "SCOPRO"))
c_es=cluster_es_vitro_small
load(system.file("extdata", "cluster_vivo_small.Rda", package = "SCOPRO"))
c_v=cluster_vivo_small
load(system.file("extdata", "marker_stages_filter.Rda", package = "SCOPRO"))
m_s_f = marker_stages_filter
load(system.file("extdata", "marker_stages.Rda", package = "SCOPRO"))
m_s = marker_stages
stages = c("Late_2_cell","epiblast_4.5","epiblast_5.5","epiblast_6.5")
output_SCOPRO = SCOPRO(n_es,n_v,c_es,c_v,"Late_2_cell",m_s_f,0.1,1,3,0.1,m_s,stages)
plot_score(output_SCOPRO,m_s,m_s_f,stages,"Late_2_cell","Score","Cluster","2-cells")