efroni_get_background_bin: Find the background bin in an expression vector

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

Description

Implements modified Efroni method for determining which bin corresponds to background expression. This method is used internally within the 'bin_expression_data“ function.

Usage

efroni_get_background_bin(expression, expression_thresh, l,
  use_original = F)

Arguments

expression	a numeric vector of expression values
expression_thresh	the threhold for determining whether a bin is in the background
l	integer, number of expression bins
use_original	logical, whether to use the original method of computing background bins (ignores minimum values). FALSE by default.

Value

an integer corresponding to the "background bin". If this bin is undetermined (no clear grouping of data), returns the maximum bin number (l)

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.