10X ATAC-seq basic quality control
Kayla Jackson and A. Sina Booeshaghi
2024-05-17
Source:vignettes/vig13_10xatac.Rmd
vig13_10xatac.RmdIntroduction
The data in this vignette is shipped with the cellatlas
repository. The count matrix and metadata are provided in the
cellatlas/examples folder as an AnnData
object. We will begin by loading the object and converting it to a
SingleCellExperiment object.
library(stringr)
library(DropletUtils)
library(Matrix)
library(SpatialExperiment)
library(SpatialFeatureExperiment)
library(scater)
library(scuttle)
library(Voyager)
library(ggplot2)
theme_set(theme_bw())
if (!file.exists("10xatac.rds"))
download.file("https://github.com/pachterlab/voyager/raw/documentation-devel/vignettes/10xatac.rds", destfile = "10xatac.rds")
sce <- readRDS("10xatac.rds")
sce <- addPerCellQCMetrics(sce)
names(colData(sce))
#> [1] "sum" "detected" "total"
plotColData(sce, "sum") +
plotColData(sce, "detected") 
plotColData(sce, x = "sum", y = "detected", bins = 100) +
scale_fill_distiller(palette = "Blues", direction = 1)
#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.
sce <- sce[, which(sce$total > 0)]
sce <- sce[rowSums(counts(sce)) > 0,]
sce
#> class: SingleCellExperiment
#> dim: 209 166
#> metadata(0):
#> assays(1): counts
#> rownames(209): 1:9410718-9410885 1:14968574-14969617 ...
#> X:119775524-119775794 X:154317937-154318131
#> rowData names(0):
#> colnames(166): AAACTCGCATTCTCGC AAAGGGCGTTGGCTTA ... TTGTCTACAGGTCCTG
#> TTTGTGTCATCGTACA
#> colData names(3): sum detected total
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):
sessionInfo()
#> R version 4.4.0 (2024-04-24)
#> Platform: x86_64-apple-darwin20
#> Running under: macOS Ventura 13.6.6
#>
#> Matrix products: default
#> BLAS: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
#>
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#>
#> time zone: UTC
#> tzcode source: internal
#>
#> attached base packages:
#> [1] stats4 stats graphics grDevices utils datasets methods
#> [8] base
#>
#> other attached packages:
#> [1] Voyager_1.6.0 scater_1.32.0
#> [3] ggplot2_3.5.1 scuttle_1.14.0
#> [5] SpatialFeatureExperiment_1.6.1 SpatialExperiment_1.14.0
#> [7] Matrix_1.7-0 DropletUtils_1.24.0
#> [9] SingleCellExperiment_1.26.0 SummarizedExperiment_1.34.0
#> [11] Biobase_2.64.0 GenomicRanges_1.56.0
#> [13] GenomeInfoDb_1.40.0 IRanges_2.38.0
#> [15] S4Vectors_0.42.0 BiocGenerics_0.50.0
#> [17] MatrixGenerics_1.16.0 matrixStats_1.3.0
#> [19] stringr_1.5.1
#>
#> loaded via a namespace (and not attached):
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#> [3] wk_0.9.1 magrittr_2.0.3
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#> [13] spdep_1.3-3 memoise_2.0.1
#> [15] DelayedMatrixStats_1.26.0 RCurl_1.98-1.14
#> [17] terra_1.7-71 htmltools_0.5.8.1
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#> [33] lifecycle_1.0.4 pkgconfig_2.0.3
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