find_ici_markers: Find Markers for ICI score computation

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

Description

Find Markers for ICI score computation

Usage

find_ici_markers(spec_table, information_level, min_spec_score = 0.15,
  transform_spec = TRUE)

Arguments

spec_table	a data.frame containing at least 4 columns: Locus Cell_Type spec (the Specificity score calculated using compute_spec_table) mean_expr (the mean expression level for that locus/cell type combination used to generated spec scores)
information_level	numeric, the maximum cumulative information level used to compute the ICI score
min_spec_score	numeric, minimum useful specification score
transform_spec	logical, whether to convert spec scores below min_spec_score to 0 (default: TRUE)

Value

Transforms the input spec_table with two additional columns:

• cumulative_sum, the cumulative sum of spec scores descending from the highest to lowest (with mean_expr used to break ties)

• is_marker whether the cumulative sum for that locus is below the information threshold specified by information_level

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.