efroni_bin: Optimize the selection of bin size for defining two...

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

Description

Optimize the selection of bin size for defining two expression classes in spec score computation.

Usage

efroni_bin(expression_data, l = 10, u = 3, use_original = F)

Arguments

expression_data	data frame (or tibble) containing the following columns for a single locus Expression (the normalized expression value, not log-transformed) Cell_Type (the cell type from which the expression data came from)
l	integer, the number of cuts to perform when binning expression values (see Efroni, et al., 2015)
u	integer, the maximum bin to consider as a background bin (0 < u < l)
use_original	logical, whether to use the original method of computing background bins (ignores minimum values). FALSE by default.

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.