compute_ici_scores: Compute ICI scores for a set of cells

In b-coli/ICITools: R Implementation of Tools for Calculating the Index of Cell Identity

Description

Compute ICI scores for a set of cells

Usage

compute_ici_scores(expression_data, spec_table, sig = FALSE,
  n_iterations = 1000, information_level = 20, min_spec_score = 0.15)

Arguments

expression_data	data frame with at least one column, "Locus", and additional columns containing expression values for each cell.
spec_table	a data.frame containing at least 4 columns: Locus Cell_Type spec (the Specificity score calculated using compute_spec_table) mean_expr (the mean expression level for that locus/cell type combination used to generated spec scores)
sig	logical, whether to compute significance scores for ici values
n_iterations	integer, number of iterations for empirical p-value computation
information_level	numeric, cumulative information score when determining marker loci
min_spec_score	minimum useful spec score for determining marker loci

Value

a data frame containing ici values and p-values for all cell/cell-type combinations.

References

Ifroni, E., Ip, PL., Nawy, T., Mello, A., Birnbaum, KD. 2015. "Quantification of cell identity from single-cell gene expression profiles". Genome Biology 16(9)

Birnbaum, KD. and Kussell, E. 2011. "Measuring cell identity in noisy biological systems". Nucl. Acids. Res. 39(21)

Examples

## Compute ICI scores for a set of test data:

# Train a spec table given initial expression data
spec_table <- compute_spec_table(expression_data = test_spec,
                                 bin_method = "Efroni",
                                 mean_method = "median",
                                 l = 5, u = 3)

# For new cell profiles, compute ICI scores
ici_scores <- compute_ici_scores(expression_data = test_ici,
                                 spec_table = spec_table,
                                 n_iterations = 1000,
                                 sig = TRUE,
                                 information_level = 10,
                                 min_spec_score = 0)

b-coli/ICITools documentation built on Dec. 27, 2021, 7:40 a.m.