README.md

switchde

Build Status

Inference of switch-like differential expression along single-cell trajectories

Installation

switchde is available on both Bioconductor and Github.

Installation from Bioconductor

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("switchde")

Installation from Github using Devtools

# install.packages("devtools") # if devtools not already installed
devtools::install_github("kieranrcampbell/switchde")

Introduction

switchde is an R package for detecting switch-like differential expression along single-cell RNA-seq trajectories. It assumes genes follow a sigmoidal pattern of gene expression and tests for differential expression using a likelihood ratio test. It also returns maximum likelihood estimates (MLE) for the sigmoid parameters, which allows filtering of genes for up or down regulation as well as where along the trajectory the regulation occurs.

The parametric form of gene expression assumed is sigmoidal:

Governed by three parameters:

Usage

switchde accepts either an SingleCellExperiment from SingleCellExperiment or a matrix of gene expression measurents. These should ideally be in log(TPM + 1) form, but any logged non-negative expression measurements will work.

We begin with an SingleCellExperiment called sce, or equivalently a gene-by-cell expression matrix X = assay(sce, "exprs"). We also require a pseudotime vector pseudotime. Then call

sde <- switchde(sce, pseudotime)

or equivalently

sde <- switchde(X, pseudotime)

This outputs a data.frame with six columns:

sde


# Source: local data frame [5,000 x 6]
# 
#                  gene         pval         qval          mu0             k        t0
#                 <chr>        <dbl>        <dbl>        <dbl>         <dbl>     <dbl>
# 1   ENSG00000225976.4 1.393383e-22 1.024546e-20 104.86694912  -0.061517122 -68.87160
# 2  ENSG00000126522.12 2.185632e-01 6.067830e-01   1.22577161  -0.018819499  45.04442
# 3   ENSG00000239917.3 9.300623e-01 1.000000e+00   0.07908401   0.013177035  45.04440
# 4  ENSG00000151413.12 8.434079e-01 1.000000e+00   1.54634312  -0.005008349  45.04431
# 5   ENSG00000163814.3 6.217089e-02 2.634360e-01   0.18162897  -0.151326785  47.80757
# 6  ENSG00000197472.10 5.324570e-05 6.969332e-04   0.46516141 -45.928518652  23.94368
# 7   ENSG00000224908.1 1.309708e-01 4.336783e-01   0.02591063 137.415319733  60.60278
# 8  ENSG00000086717.13 8.203174e-02 3.190731e-01   0.04509236 256.638830394  49.59851
# 9   ENSG00000215183.4 2.127059e-01 5.991007e-01   0.02842577  -0.900165012  46.86811
# 10  ENSG00000127884.4 7.516905e-01 1.000000e+00   5.62698376   0.001580912  45.04440
# ..                ...          ...          ...          ...           ...       ...

with columns:

We can also extract the parameters and plot the results:

gene <- sde$gene[1]
pars <- extract_pars(sde, gene)
print(pars)

#          mu0            k           t0 
# 104.86694912  -0.06151712 -68.87160316 

switchplot(exprs(sce)[gene, ], pseudotime, pars)

Authors

Kieran Campbell & Christopher Yau

Wellcome Trust Centre for Human Genetics, University of Oxford



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switchde documentation built on Nov. 8, 2020, 5:19 p.m.