Get list of expressed genes for each assay using same filters as processAssays().
Usage
getExprGeneNames(
sceObj,
assays = assayNames(sceObj),
min.cells = 5,
min.count = 5,
min.samples = 4,
min.prop = 0.4,
min.total.count = 15,
normalize.method = "TMM"
)Arguments
- sceObj
SingleCellExperiment object
- assays
array of assay names to include in analysis. Defaults to
assayNames(sceObj)- min.cells
minimum number of observed cells for a sample to be included in the analysis
- min.count
minimum number of reads for a gene to be considered expressed in a sample. Passed to
edgeR::filterByExpr- min.samples
minimum number of samples passing cutoffs for cell cluster to be retained
- min.prop
minimum proportion of retained samples with non-zero counts for a gene to be retained
- min.total.count
minimum total count required per gene for inclusion
- normalize.method
normalization method to be used by
calcNormFactors
Examples
library(muscat)
data(example_sce)
# create pseudobulk for each sample and cell cluster
pb <- aggregateToPseudoBulk(example_sce,
assay = "counts",
sample_id = "sample_id",
cluster_id = "cluster_id",
verbose = FALSE
)
# Gene expressed genes for each cell type
geneList = getExprGeneNames(pb)
# Create precision weights for pseudobulk
# By default, weights are set to cell count,
# which is the default in processAssays()
# even when no weights are specified
weightsList <- pbWeights(example_sce,
sample_id = "sample_id",
cluster_id = "cluster_id",
geneList = geneList
)
#> Processing: B cells
#> Computing library sizes...
#> Processing samples...
#> Processing: CD14+ Monocytes
#> Computing library sizes...
#> Processing samples...
#> Processing: CD4 T cells
#> Computing library sizes...
#> Processing samples...
#> Processing: CD8 T cells
#> Computing library sizes...
#> Processing samples...
#> Processing: FCGR3A+ Monocytes
#> Computing library sizes...
#> Processing samples...
# voom-style normalization using initial weights
res.proc <- processAssays(pb, ~group_id, weightsList = weightsList)
#> B cells...
#> 0.27 secs
#> CD14+ Monocytes...
#> 0.37 secs
#> CD4 T cells...
#> 0.32 secs
#> CD8 T cells...
#> 0.17 secs
#> FCGR3A+ Monocytes...
#> 0.4 secs