intensity2circle: Infer angles for each single-cell samples using fluorescence...

In peco: A Supervised Approach for **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data

Description

We use FUCCI intensities to infer the position of the cells in cell cycle progression. The result is a vector of angles on a unit circle corresponding to the positions of the cells in cell cycle progression.

Usage

intensity2circle(mat, plot.it = FALSE, method = c("trig", "algebraic"))

Arguments

mat	A matrix of two columns of summarized fluorescence intensity. Rows correspond to samples.
plot.it	TRUE or FALSE. Plot the fitted results.
method	The method used to fit the circle. trig uses trignometry to transform intensity measurements from cartesian coordinates to polar coordinates. algebraic uses an algebraic approach for circle fitting, using the conicfit package.

Value

The inferred angles on unit circle based on the input intensity measurements.

Author(s)

Joyce Hsiao

Examples

# use our data
library(SingleCellExperiment)
data(sce_top101genes)

# FUCCI scores - log10 transformed sum of intensities that were
# corrected for background noise
ints <- colData(sce_top101genes)[,c("rfp.median.log10sum.adjust",
                          "gfp.median.log10sum.adjust")]
intensity2circle(ints, plot.it=TRUE, method = "trig")

peco documentation built on Nov. 8, 2020, 8:16 p.m.