Modeling continuous cell-level covariates
Collapse using mean value for pseudobulk data
Developed by Gabriel Hoffman
Run on 2024-05-14 15:49:06
Source:vignettes/cell_covs.Rmd
cell_covs.RmdIntroduction
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).
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$StimStatus <- sce$stimIn 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:
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 0.127 0.0241
## 2 B cells ctrl1015 4.00 -0.0539 -0.00302
## 3 B cells ctrl1016 4 0.00571 0.0366
## 4 B cells ctrl1039 4.04 -0.102 -0.0970
## 5 B cells ctrl107 4 0.0438 0.0163
## 6 B cells ctrl1244 4 -0.0928 0.138
## 7 B cells ctrl1256 4.01 0.0344 -0.0432
## 8 B cells ctrl1488 4.02 -0.0599 -0.00684
## 9 B cells stim101 4.09 0.128 0.0350
## 10 B cells stim1015 4.06 0.0267 0.0681
## # ℹ 118 more rowsAnalysis
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)
# Differential expression analysis within each assay
res.dl <- dreamlet(res.proc, form)
# dreamlet results include coefficients for value1 and value2
res.dl## class: dreamletResult
## assays(8): B cells CD14+ Monocytes ... Megakaryocytes NK cells
## Genes:
## min: 164
## max: 5262
## details(7): assay n_retain ... n_errors error_initial
## coefNames(4): (Intercept) StimStatusstim value1 value2Session Info
## R version 4.3.0 (2023-04-21)
## Platform: x86_64-apple-darwin22.4.0 (64-bit)
## Running under: macOS Ventura 13.5
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## BLAS: /Users/gabrielhoffman/prog/R-4.3.0/lib/libRblas.dylib
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