compute_ici_for_cell: Compute ici score for all cell types for a given cell's...

Description Usage Arguments Value References

View source: R/compute_ici.R

Description

Compute ici score for all cell types for a given cell's expression profile

Usage

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compute_ici_for_cell(expression_and_marker_data, sig = FALSE,
  n_iterations = 1000)

Arguments

expression_and_marker_data

data.frame with the following columns for each cell type (melted):

  • Locus, the gene name

  • Cell_Type, the cell type for each Locus/Expression/spec/is_marker combination

  • is_marker, logical, whether each gene is a marker

  • Expression, numeric, the expression of each locus for this profile

  • spec, numeric, the specificity score for this each locus for the cell type in question.

sig

logical, whether to compute p-values for ici scores

n_iterations

integer, how many random permutations for p-value calculations

Value

a data.frame with three columns:

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)


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