Run batch correction, followed by:
stashing of batches in metadata 'batch'
clustering with resolution 0.2 to 2.0 in increments of 0.2
saving to <proj_dir>/output/sce/
sce .rds
Usage
sce_integrate(
sce_list,
resolution = seq(0.2, 1, by = 0.2),
suffix = "",
organism = "human",
batch_correct = TRUE,
annotate_cell_cycle = FALSE,
annotate_percent_mito = FALSE,
reduction = "corrected",
...
)Arguments
- sce_list
List of objects to be integrated
- resolution
Range of resolution
- suffix
a suffix to be appended to a file save in output dir
- organism
Default "human"
- batch_correct
whether to integrate by batch correction
- annotate_cell_cycle
whether to score cell cycle phases
- annotate_percent_mito
logical scalar whether to annotate mitochondrial percentage
- reduction
pca, umap, or tsne
- ...
extra args passed to integrate
Examples
data("tiny_sce")
tiny_sce |>
splitByCol("bath") |>
sce_integrate(resolution = 0.2, batch_correct = FALSE)
#> NULL