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‘lmer’ method in Zlm function obviates first factor level #195
Description
I wonder whether the behavior of ‘lmer’ method in zlm can be explained to understand why, despite using the model form (~ 0 + …), the first level of a factor is missing. See below for a reproducible example. This prevents the design of specific contrasts later on while using for instance getLogFC function.
• [x] I have searched existing MAST issues
• [x] I’m using MAST version 1.30.0
• [x] I can provide a reproducible example
Reproducible example
library(muscat)
library(SingleCellExperiment)
# Load data
data(example_sce)
head(colData(example_sce))
# To SingleCellAssay
sca <- SceToSingleCellAssay(example_sce, class = "SingleCellAssay")
cdr2 <- colSums(assay(sca)>0)
colData(sca)$ngeneson <- scale(cdr2)
# Prepare metadata
colData(sca)$cluster_id <- sub(" ", "_", sca$cluster_id)
colData(sca)$cluster_id <- sub("T cells", "T_cells", sca$cluster_id)
table(colData(sca)$cluster_id)
colData(sca)$sample_id <- sub(" ", "_", sca$sample_id)
colData(sca)$cluster_id <-factor(colData(sca)$cluster_id)
colData(sca)$sample_id <-factor(colData(sca)$sample_id)
# Level order
#levels(colData(sca)$cluster_id) equals to "B_cells" "CD14+_Monocytes" "CD4_T_cells" "CD8_T_cells" "FCGR3A+_Monocytes"
colData(sca)$cluster_id <- factor(
colData(sca)$cluster_id,
levels = levels(colData(sca)$cluster_id)
)
# Fit the model
form = ~ 0 + cluster_id + ngeneson + (1|sample_id)
zlmCond <- zlm(formula = form,
sca=sca,
method='lmer',
ebayes=F,
strictConvergence=F,
fitArgsD=list(nAGQ = 0))
colnames(zlmCond@coefD) # B_cells excluded
# Re-level order for comparison
colData(sca)$cluster_id <- factor(
colData(sca)$cluster_id,
levels = rev(levels(colData(sca)$cluster_id)) # FCGR3A+_Monocytes first (ref) level now
)
zlmCond2 <- zlm(formula = form,
sca=sca,
method='lmer',
ebayes=F,
strictConvergence=F,
fitArgsD=list(nAGQ = 0))
colnames(zlmCond2@coefD) # FCGR3A+_Monocytes excluded
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