intensity2circle: Infer Angles for Single-cell Samples Using Fluorescence...

In jhsiao999/peco: A Supervised Approach for Predicting Cell Cycle Progression Using Single-Cell RNA-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 with two columns giving summarized fluorescence intensities. Rows correspond to samples.
plot.it	TRUE or FALSE. If plot.it = TRUE, plot the fitted results.
method	The method used to fit the circle. method = "trig" uses trignometry to transform intensity measurements from cartesian coordinates to polar coordinates; method = "algebraic" uses an algebraic approach for circle fitting, implemented in the conicfit package.

Value

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

Author(s)

Joyce Hsiao

Examples

library(SingleCellExperiment)
data(sce_top101genes)

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

jhsiao999/peco documentation built on Nov. 21, 2020, 5:34 p.m.