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)
sce <- LawlorPancreasData()
snapshotDate(): 2020-10-27
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
loading from cache
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
loading from cache
edb <- AnnotationHub()[["AH73881"]]
snapshotDate(): 2020-10-27
loading from cache
require("ensembldb")
anno <- select(
  edb, 
  keys = rownames(sce), 
  keytype = "GENEID", 
  columns = c("SYMBOL", "SEQNAME")
)
rowData(sce) <- anno[match(rownames(sce), anno[, 1]), -1]
stats <- perCellQCMetrics(
  sce, 
  subsets = list(Mito = which(rowData(sce)$SEQNAME == "MT"))
)
qc <- quickPerCellQC(
  stats, 
  percent_subsets = "subsets_Mito_percent",
  batch = sce$`islet unos id`
)
sce <- sce[, !qc$discard]
set.seed(1000)
clusters <- quickCluster(sce)
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm):
collapsing to unique 'x' values
sce <- computeSumFactors(sce, clusters = clusters)
sce <- logNormCounts(sce)
dec_sce <- modelGeneVarByPoisson(sce)
# Select the top 10000 genes.
top_sce <- getTopHVGs(dec_sce, n = 10000)
sce <- sce[top_sce, ]
# Running PCA is slow.
sce <- runPCA(sce)
sce <- runTSNE(sce, dimred = "PCA")
sce <- runUMAP(sce, dimred = "PCA")
plotPCA(sce, colour_by = "cell type")

plotTSNE(sce, colour_by = "cell type")

The subset will be the Alpha cells.

alpha_cell_mask <- which(colData(sce)[["cell type"]] == "Alpha")
sce_subset <- sce[, alpha_cell_mask]
saveRDS(sce_subset, file = here::here("data", "lawlor.rds"))
saveRDS(sce, file = here::here("data", "lawlor_full.rds"))

devtools::session_info()
─ 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 ───────────────────────────────────────────────────────────────────
 package                * version  date       lib source        
 AnnotationDbi          * 1.52.0   2020-10-27 [1] Bioconductor  
 AnnotationFilter       * 1.14.0   2020-10-27 [1] Bioconductor  
 AnnotationHub          * 2.22.0   2020-10-27 [1] Bioconductor  
 askpass                  1.1      2019-01-13 [2] CRAN (R 4.0.3)
 assertthat               0.2.1    2019-03-21 [2] CRAN (R 4.0.3)
 beachmat                 2.6.4    2020-12-20 [1] Bioconductor  
 beeswarm                 0.3.1    2021-03-07 [1] CRAN (R 4.0.0)
 Biobase                * 2.50.0   2020-10-27 [1] Bioconductor  
 BiocFileCache          * 1.14.0   2020-10-27 [1] Bioconductor  
 BiocGenerics           * 0.36.0   2020-10-27 [2] Bioconductor  
 BiocManager              1.30.10  2019-11-16 [1] CRAN (R 4.0.0)
 BiocNeighbors            1.8.2    2020-12-07 [1] Bioconductor  
 BiocParallel             1.24.1   2020-11-06 [2] Bioconductor  
 BiocSingular             1.6.0    2020-10-27 [1] Bioconductor  
 BiocVersion              3.12.0   2020-04-27 [1] Bioconductor  
 biomaRt                  2.46.3   2021-02-09 [1] Bioconductor  
 Biostrings               2.58.0   2020-10-27 [2] Bioconductor  
 bit                      4.0.4    2020-08-04 [1] CRAN (R 4.0.0)
 bit64                    4.0.5    2020-08-30 [1] CRAN (R 4.0.0)
 bitops                   1.0-6    2013-08-17 [2] CRAN (R 4.0.3)
 blob                     1.2.1    2020-01-20 [1] CRAN (R 4.0.0)
 bluster                  1.0.0    2020-10-27 [1] Bioconductor  
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 callr                    3.5.1    2020-10-13 [2] CRAN (R 4.0.3)
 cli                      2.2.0    2020-11-20 [2] CRAN (R 4.0.3)
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 curl                     4.3      2019-12-02 [2] CRAN (R 4.0.3)
 DBI                      1.1.1    2021-01-15 [1] CRAN (R 4.0.0)
 dbplyr                 * 2.1.0    2021-02-03 [1] CRAN (R 4.0.0)
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 DelayedMatrixStats       1.12.3   2021-02-03 [1] Bioconductor  
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 devtools                 2.3.2    2020-09-18 [2] CRAN (R 4.0.3)
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 dplyr                    1.0.5    2021-03-05 [1] CRAN (R 4.0.0)
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 ExperimentHub            1.16.0   2020-10-27 [1] Bioconductor  
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 fastmap                  1.1.0    2021-01-25 [1] CRAN (R 4.0.0)
 FNN                      1.1.3    2019-02-15 [1] CRAN (R 4.0.0)
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 GenomeInfoDbData         1.2.4    2020-12-30 [2] Bioconductor  
 GenomicAlignments        1.26.0   2020-10-27 [1] Bioconductor  
 GenomicFeatures        * 1.42.2   2021-03-12 [1] Bioconductor  
 GenomicRanges          * 1.42.0   2020-10-27 [2] Bioconductor  
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 glue                     1.4.2    2020-08-27 [2] CRAN (R 4.0.3)
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 here                     1.0.1    2020-12-13 [1] CRAN (R 4.0.0)
 hms                      1.0.0    2021-01-13 [1] CRAN (R 4.0.0)
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 httpuv                   1.5.5    2021-01-13 [1] CRAN (R 4.0.0)
 httr                     1.4.2    2020-07-20 [2] CRAN (R 4.0.3)
 igraph                   1.2.6    2020-10-06 [1] CRAN (R 4.0.0)
 interactiveDisplayBase   1.28.0   2020-10-27 [1] Bioconductor  
 IRanges                * 2.24.1   2020-12-12 [2] Bioconductor  
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 jsonlite                 1.7.2    2020-12-09 [2] CRAN (R 4.0.3)
 knitr                    1.30     2020-09-22 [2] CRAN (R 4.0.3)
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 magrittr                 2.0.1    2020-11-17 [2] CRAN (R 4.0.3)
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[1] /home/jpullin/R_libs
[2] /opt/R/4.0.3/lib/R/library