efroni_get_binsizes: Get binsize range for optimization

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

Description

If the number of cuts to test are specified, compute the range of possible bin sizes as close to the transition to "background" expression as possible. If the number of cuts is not specified, attempts to optimize the binsize across the whole range of gene expression values (50 evenly spaced binsizes).

Usage

efroni_get_binsizes(expression, background_bin, l)

Arguments

expression	numeric, expression vector
background_bin	pre-computed background bin. If NA, whole expression range is considered.
l	number of cuts (bins). If < 1, whole expression range is considered.

Value

a vector of 50 bin sizes to iterate over.

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.