Human pancreatic islet cell datasets produced across four technologies,
SMART-Seq2 (E-MTAB-5061), CelSeq (GSE81076), CelSeq2 (GSE85241), and Fluidigm C1 (GSE86469),
from SeuratData package.
For each data set in panc8
, 200 cells were downsampled to form the panc8_sub
dataset.
Examples
if (FALSE) { # \dontrun{
if (interactive()) {
data(pancreas_sub)
if (!require("SeuratData", quietly = TRUE)) {
pak::pak("satijalab/seurat-data")
}
library(SeuratData)
library(Seurat)
InstallData("panc8")
data(panc8)
panc8 <- UpdateSeuratObject(panc8)
set.seed(98)
cells_sub <- unlist(
lapply(
split(colnames(panc8), panc8$dataset),
function(x) sample(x, size = 200)
)
)
panc8_sub <- subset(panc8, cells = cells_sub)
counts <- GetAssayData5(
panc8_sub,
layer = "counts",
verbose = FALSE
)
panc8_sub <- CreateSeuratObject(
counts = counts,
meta.data = panc8_sub@meta.data
)
panc8_sub <- panc8_sub[Matrix::rowSums(counts) > 0, ]
panc8_sub <- panc8_sub[toupper(
rownames(panc8_sub)
) %in% toupper(
rownames(pancreas_sub)
), ]
panc8_sub$celltype <- gsub("_", "-", panc8_sub$celltype)
panc8_sub$celltype <- gsub(" ", "-", panc8_sub$celltype)
usethis::use_data(
panc8_sub,
compress = "xz",
overwrite = TRUE
)
}
} # }