compute_spec: Compute Specification Score

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

Description

For expression data for a given locus, calculates the specificity score, as outlined in Birnbaum, et al., 2011. Supports any number of bins, which MUST be specified in the 'bin' column of the input object.

Usage

compute_spec(binned_expression_data)

Arguments

binned_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) bin (which expression bin the expression for this locus falls in per dataset)

Value

A tibble with cell-type specific spec scores for this locus. Supports negative spec scores (determined by whether the mean expression for that cell type is above/below the mean expression over all data sets.)

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.