Last updated: 2021-04-13
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Knit directory: mage_2020_marker-gene-benchmarking/
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File | Version | Author | Date | Message |
---|---|---|---|---|
Rmd | b5b2a88 | Jeffrey Pullin | 2021-04-13 | Add new results |
Rmd | ecca831 | Jeffrey Pullin | 2021-03-29 | Finish lawlor data processing |
Rmd | 797e05b | Jeffrey Pullin | 2021-03-28 | Add partial processing of lawlor data |
library(scRNAseq)
library(AnnotationHub)
library(scater)
library(scran)
<- LawlorPancreasData() sce
snapshotDate(): 2020-10-27
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
loading from cache
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
loading from cache
<- AnnotationHub()[["AH73881"]] edb
snapshotDate(): 2020-10-27
loading from cache
require("ensembldb")
<- select(
anno
edb, keys = rownames(sce),
keytype = "GENEID",
columns = c("SYMBOL", "SEQNAME")
)rowData(sce) <- anno[match(rownames(sce), anno[, 1]), -1]
<- perCellQCMetrics(
stats
sce, subsets = list(Mito = which(rowData(sce)$SEQNAME == "MT"))
)<- quickPerCellQC(
qc
stats, percent_subsets = "subsets_Mito_percent",
batch = sce$`islet unos id`
)<- sce[, !qc$discard] sce
set.seed(1000)
<- quickCluster(sce) clusters
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm):
collapsing to unique 'x' values
<- computeSumFactors(sce, clusters = clusters)
sce <- logNormCounts(sce) sce
<- modelGeneVarByPoisson(sce)
dec_sce # Select the top 10000 genes.
<- getTopHVGs(dec_sce, n = 10000)
top_sce <- sce[top_sce, ] sce
# Running PCA is slow.
<- runPCA(sce)
sce <- runTSNE(sce, dimred = "PCA")
sce <- runUMAP(sce, dimred = "PCA") sce
plotPCA(sce, colour_by = "cell type")
plotTSNE(sce, colour_by = "cell type")
The subset will be the Alpha cells.
<- which(colData(sce)[["cell type"]] == "Alpha")
alpha_cell_mask <- sce[, alpha_cell_mask]
sce_subset saveRDS(sce_subset, file = here::here("data", "lawlor.rds"))
saveRDS(sce, file = here::here("data", "lawlor_full.rds"))
::session_info() devtools
─ Session info ───────────────────────────────────────────────────────────────
setting value
version R version 4.0.3 (2020-10-10)
os CentOS Linux 7 (Core)
system x86_64, linux-gnu
ui X11
language (EN)
collate en_AU.UTF-8
ctype en_AU.UTF-8
tz UTC
date 2021-04-13
─ Packages ───────────────────────────────────────────────────────────────────
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