calculate_metrics: Calculate metrics through pseudotime

In kieranrcampbell/embeddr: Laplacian eigenmaps & principal curves for pseudotemporal ordering of single-cell RNA-seq data

Description

Calculate various metrics (mean, variance, CV2 and signal-to-noise ratio) using a sliding window approach

Usage

calculate_metrics(sce, gene, window_size = NULL)

Arguments

sce	A SCESet object
gene	The gene of interest on which to calculate the metrics
window_size	The size of the sliding window. By default taken to be half the number of cells

Value

An object of class 'data.frame' where each column is a metric (window-averaged pseudotime, mean, variance, CV2, signal to noise ratio)

Examples

library(scater)
data('sc_example_counts') ; sce <- newSCESet(countData = sc_example_counts)
sce <- embeddr(sce)
sce <- fit_pseudotime(sce)
metrics <- calculate_metrics(sce, 1)

kieranrcampbell/embeddr documentation built on May 20, 2019, 9:24 a.m.