pseudotime_test: Pseudotime gene testing

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

Description

This function fits both smoothing B-spline tobit regression models for all genes in sce and computes p-values by comparing to the null model using a likelihood ratio test.

Usage

pseudotime_test(sce, n_cores = 2)

Arguments

sce	An object of class SCESet. If only a certain number of genes are desired to be tested then sce must be subsetted before the function call.
n_cores	The number of cores used in the call to mcapply

Value

A data.frame with three columns: the gene name, the unadjusted p-value and the Benjamini-Hochberg adjusted q-value. Note that different multiple testing corrections can be applied using the R function p.adjust.

Examples

library(scater)
data('sc_example_counts') ; sce <- newSCESet(countData = sc_example_counts)
sce <- embeddr(sce)
sce <- fit_pseudotime(sce)
df_pval <- pseudotime_test(sce[1:4,]) # only for first four genes

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