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

intensity2circle {peco}

R Documentation

Infer angles for each single-cell samples using fluorescence intensities

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")

[Package peco version 1.0.0 Index]