compute_ici_pval: Compute p-values for a single expression/cell type profile...
In b-coli/ICITools: R Implementation of Tools for Calculating the Index of Cell Identity
Description
Usage
Arguments
Value
References
Description
Compute p-values for a single expression/cell type profile (Internal)
Usage
1
compute_ici_pval(cell_type_data, ici_score = NULL, n_iterations = 1000)
Arguments
cell_type_data
a data.frame with the following columns:
Locus, the gene name
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.
ici_score
numeric, the ici score to compare the random iterations against.
If null (default), will compute denovo
n_iterations,
integer, number of random iterations
Value
numeric, raw p-value indicating the number of randomized ici scores
that are greater than or equal to the "real" ici score.
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.
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Description Usage Arguments Value References
Description
Compute p-values for a single expression/cell type profile (Internal)
Usage
1 | compute_ici_pval(cell_type_data, ici_score = NULL, n_iterations = 1000)
|
Arguments
cell_type_data |
a data.frame with the following columns:
|
ici_score |
numeric, the ici score to compare the random iterations against. If null (default), will compute denovo |
n_iterations, |
integer, number of random iterations |
Value
numeric, raw p-value indicating the number of randomized ici scores that are greater than or equal to the "real" ici score.
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)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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