Description Usage Arguments Value References
Compute ici score for all cell types for a given cell's expression profile
1 2 | compute_ici_for_cell(expression_and_marker_data, sig = FALSE,
n_iterations = 1000)
|
expression_and_marker_data |
data.frame with the following columns for each cell type (melted):
|
sig |
logical, whether to compute p-values for ici scores |
n_iterations |
integer, how many random permutations for p-value calculations |
a data.frame with three columns:
Cell_Type, the cell type for each Locus/Expression/spec/is_marker combination type in question.
ici_score the ici score for that cell/cell-type
p-val the p-value associated with the ici-score, NA if sig = FALSE.
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)
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