1 Introduction

Since read counts are summed across cells in a pseudobulk approach, modeling continuous cell-level covariates also requires a collapsing step. Here we summarize the values of a variable from a set of cells using the mean, and store the value for each cell type. Including these variables in a regression formula uses the summarized values from the corresponding cell type.

We demonstrate this feature on a lightly modified analysis of PBMCs from 8 individuals stimulated with interferon-β (Kang, et al, 2018, Nature Biotech).

2 Standard processing

Here is the code from the main vignette:

library(dreamlet)
library(muscat)
library(ExperimentHub)
library(scater)

# Download data, specifying EH2259 for the Kang, et al study
eh <- ExperimentHub()
sce <- eh[["EH2259"]]

# only keep singlet cells with sufficient reads
sce <- sce[rowSums(counts(sce) > 0) > 0, ]
sce <- sce[, colData(sce)$multiplets == "singlet"]

# compute QC metrics
qc <- perCellQCMetrics(sce)

# remove cells with few or many detected genes
ol <- isOutlier(metric = qc$detected, nmads = 2, log = TRUE)
sce <- sce[, !ol]

# set variable indicating stimulated (stim) or control (ctrl)
sce$StimStatus <- sce$stim

In many datasets, continuous cell-level variables could be mapped reads, gene count, mitochondrial rate, etc. There are no continuous cell-level variables in this dataset, so we can simulate two from a normal distribution:

sce$value1 <- rnorm(ncol(sce))
sce$value2 <- rnorm(ncol(sce))

3 Pseudobulk

Now compute the pseudobulk using standard code:

sce$id <- paste0(sce$StimStatus, sce$ind)

# Create pseudobulk
pb <- aggregateToPseudoBulk(sce,
  assay = "counts",
  cluster_id = "cell",
  sample_id = "id",
  verbose = FALSE
)

The means per variable, cell type, and sample are stored in the pseudobulk SingleCellExperiment object:

metadata(pb)$aggr_means
## # A tibble: 128 × 5
## # Groups:   cell [8]
##    cell    id       cluster   value1   value2
##    <fct>   <fct>      <dbl>    <dbl>    <dbl>
##  1 B cells ctrl101     3.96 -0.115    0.0163 
##  2 B cells ctrl1015    4.00 -0.0253  -0.0851 
##  3 B cells ctrl1016    4    -0.0199  -0.110  
##  4 B cells ctrl1039    4.04 -0.0802   0.124  
##  5 B cells ctrl107     4     0.0450  -0.0659 
##  6 B cells ctrl1244    4     0.0620   0.124  
##  7 B cells ctrl1256    4.01 -0.00526 -0.0785 
##  8 B cells ctrl1488    4.02  0.153    0.0449 
##  9 B cells stim101     4.09  0.0694  -0.00990
## 10 B cells stim1015    4.06  0.0122  -0.0229 
## # ℹ 118 more rows

4 Analysis

Including these variables in a regression formula uses the summarized values from the corresponding cell type. This happens behind the scenes, so the user doesn’t need to distinguish bewteen sample-level variables stored in colData(pb) and cell-level variables stored in metadata(pb)$aggr_means.

Variance partition and hypothesis testing proceeds as ususal:

form <- ~ StimStatus + value1 + value2

# Normalize and apply voom/voomWithDreamWeights
res.proc <- processAssays(pb, form, min.count = 5)

# run variance partitioning analysis
vp.lst <- fitVarPart(res.proc, form)

# Summarize variance fractions genome-wide for each cell type
plotVarPart(vp.lst, label.angle = 60)