bin_expression_data: Compute bins for expression data

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

Description

takes in expression and cell-type data for a single locus, and computes expression bins.

Usage

bin_expression_data(expression_data, method = "Efroni", ...)

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)
method	a character (possible values consist only of "Efroni" for now) OR a function that takes in the 'expression_data' data.frame object and any other parameters, and returns expression_data with an extra column, "bin" containing the expression bin for that dataset/cell_type combination
...	Additional parameters to the 'method' function argument, if specified

Value

a data.frame (or tibble) containing the data within 'expression_data' and an additional "bin" column describing the expression bin for that expression/cell_type combination.

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.