scuttle 1.4.0
scuttle provides various low-level utilities for single-cell RNA-seq data analysis, typically used at the start of the analysis workflows or within high-level functions in other packages. This vignette will discuss the use of miscellaneous functions for scRNA-seq data processing. To demonstrate, we will obtain the classic Zeisel dataset from the scRNAseq package, and apply some quick quality control to remove damaged cells.
library(scRNAseq)
sce <- ZeiselBrainData()
library(scuttle)
sce <- quickPerCellQC(sce, subsets=list(Mito=grep("mt-", rownames(sce))),
sub.fields=c("subsets_Mito_percent", "altexps_ERCC_percent"))
sce## class: SingleCellExperiment
## dim: 20006 2816
## metadata(0):
## assays(1): counts
## rownames(20006): Tspan12 Tshz1 ... mt-Rnr1 mt-Nd4l
## rowData names(1): featureType
## colnames(2816): 1772071015_C02 1772071017_G12 ... 1772063068_D01
## 1772066098_A12
## colData names(27): tissue group # ... high_altexps_ERCC_percent discard
## reducedDimNames(0):
## mainExpName: endogenous
## altExpNames(2): ERCC repeatNote: A more comprehensive description of the use of scuttle functions (along with other packages) in a scRNA-seq analysis workflow is available at https://osca.bioconductor.org.
The aggregateAcrossCells() function is helpful for aggregating expression values across groups of cells.
For example, we might wish to sum together counts for all cells in the same cluster,
possibly to use as a summary statistic for downstream analyses (e.g., for differential expression with edgeR).
This will also perform the courtesy of sensibly aggregating the column metadata for downstream use.
library(scuttle)
agg.sce <- aggregateAcrossCells(sce, ids=sce$level1class)
head(assay(agg.sce))## astrocytes_ependymal endothelial-mural interneurons microglia
## Tspan12 71 120 186 13
## Tshz1 89 58 335 41
## Fnbp1l 73 102 689 29
## Adamts15 2 14 64 0
## Cldn12 45 23 160 4
## Rxfp1 0 3 74 0
## oligodendrocytes pyramidal CA1 pyramidal SS
## Tspan12 93 269 58
## Tshz1 293 65 331
## Fnbp1l 230 857 1054
## Adamts15 19 11 15
## Cldn12 206 410 273
## Rxfp1 13 48 30colData(agg.sce)[,c("ids", "ncells")]## DataFrame with 7 rows and 2 columns
## ids ncells
## <character> <integer>
## astrocytes_ependymal astrocytes_ependymal 179
## endothelial-mural endothelial-mural 160
## interneurons interneurons 290
## microglia microglia 78
## oligodendrocytes oligodendrocytes 774
## pyramidal CA1 pyramidal CA1 938
## pyramidal SS pyramidal SS 397It is similarly possible to sum across multiple factors, as shown below for the cell type and the tissue of origin. This yields one column per combination of cell type and tissue, which allows us to conveniently perform downstream analyses with both factors.
agg.sce <- aggregateAcrossCells(sce,
ids=colData(sce)[,c("level1class", "tissue")])
head(assay(agg.sce))## [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
## Tspan12 22 49 9 111 52 134 0 13 10 83 269 58
## Tshz1 37 52 7 51 90 245 1 40 50 243 65 331
## Fnbp1l 22 51 6 96 227 462 3 26 18 212 857 1054
## Adamts15 0 2 2 12 15 49 0 0 0 19 11 15
## Cldn12 4 41 0 23 61 99 0 4 22 184 410 273
## Rxfp1 0 0 0 3 3 71 0 0 1 12 48 30colData(agg.sce)[,c("level1class", "tissue", "ncells")]## DataFrame with 12 rows and 3 columns
## level1class tissue ncells
## <character> <character> <integer>
## 1 astrocytes_ependymal ca1hippocampus 71
## 2 astrocytes_ependymal sscortex 108
## 3 endothelial-mural ca1hippocampus 25
## 4 endothelial-mural sscortex 135
## 5 interneurons ca1hippocampus 126
## ... ... ... ...
## 8 microglia sscortex 64
## 9 oligodendrocytes ca1hippocampus 120
## 10 oligodendrocytes sscortex 654
## 11 pyramidal CA1 ca1hippocampus 938
## 12 pyramidal SS sscortex 397Summation across rows may occasionally be useful for obtaining a measure of the activity of a gene set, e.g., in a pathway.
Given a list of gene sets, we can use the sumCountsAcrossFeatures() function to aggregate expression values across features.
This is usually best done by averaging the log-expression values as shown below.
sce <- logNormCounts(sce)
agg.feat <- sumCountsAcrossFeatures(sce,
ids=list(GeneSet1=1:10, GeneSet2=11:50, GeneSet3=1:100),
average=TRUE, exprs_values="logcounts")
agg.feat[,1:10]## 1772071015_C02 1772071017_G12 1772071017_A05 1772071014_B06
## GeneSet1 0.7888973 0.2245293 0.7733931 0.5526122
## GeneSet2 1.0788281 1.0130457 1.2797820 1.1705150
## GeneSet3 1.1622245 1.0207948 1.2963940 1.2230518
## 1772067065_H06 1772071017_E02 1772067065_B07 1772067060_B09
## GeneSet1 0.5092772 0.3630931 0.5399704 0.07722382
## GeneSet2 1.2223993 1.3115876 1.3146717 1.20420279
## GeneSet3 1.1451365 1.1792717 1.1287984 1.15725115
## 1772071014_E04 1772071015_D04
## GeneSet1 0.7433737 0.8076824
## GeneSet2 1.1949143 1.3117134
## GeneSet3 1.0300578 1.2069146Similar functions are available to compute the number or proportion of cells with detectable expression in each group. To wit:
agg.n <- summarizeAssayByGroup(sce, statistics="prop.detected",
ids=colData(sce)[,c("level1class", "tissue")])
head(assay(agg.n))## [,1] [,2] [,3] [,4] [,5] [,6] [,7]
## Tspan12 0.21126761 0.17592593 0.20 0.34074074 0.28571429 0.3597561 0.00000000
## Tshz1 0.22535211 0.16666667 0.20 0.17777778 0.36507937 0.4756098 0.07142857
## Fnbp1l 0.16901408 0.18518519 0.16 0.30370370 0.63492063 0.7500000 0.14285714
## Adamts15 0.00000000 0.01851852 0.08 0.04444444 0.04761905 0.1768293 0.00000000
## Cldn12 0.04225352 0.14814815 0.00 0.06666667 0.29365079 0.3658537 0.00000000
## Rxfp1 0.00000000 0.00000000 0.00 0.01481481 0.01587302 0.2134146 0.00000000
## [,8] [,9] [,10] [,11] [,12]
## Tspan12 0.109375 0.058333333 0.07492355 0.188699360 0.09068010
## Tshz1 0.171875 0.216666667 0.20336391 0.051172708 0.33753149
## Fnbp1l 0.234375 0.075000000 0.15596330 0.459488273 0.72040302
## Adamts15 0.000000 0.000000000 0.01529052 0.009594883 0.02267003
## Cldn12 0.046875 0.141666667 0.15137615 0.287846482 0.35516373
## Rxfp1 0.000000 0.008333333 0.01223242 0.039445629 0.04785894Normally, sparse matrices are provided in the MatrixMarket (.mtx) format,
where they can be read efficiently into memory using the readMM() function from the Matrix package.
However, for some reason, it has been popular to save these files in dense form as tab- or comma-separate files.
This is an inefficient and inconvenient approach, requiring users to read in the entire dataset in dense form with functions like read.delim() or read.csv() (and hope that they have enough memory on their machines to do so).
In such cases, scuttle provides the readSparseCounts() function to overcome excessive memory requirements.
This reads in the dataset in a chunkwise manner, progressively coercing each chunk into a sparse format and combining them into a single sparse matrix to be returned to the user.
In this manner, we never attempt to load the entire dataset in dense format to memory.
# Mocking up a dataset to demonstrate:
outfile <- tempfile()
write.table(counts(sce)[1:100,], file=outfile, sep="\t", quote=FALSE)
# Reading it in as a sparse matrix:
output <- readSparseCounts(outfile)
class(output)## [1] "dgCMatrix"
## attr(,"package")
## [1] "Matrix"When publishing a dataset, the best practice is to provide gene annotations in the form of a stable identifier like those from Ensembl or Entrez. This provides an unambiguous reference to the identity of the gene, avoiding difficulties with synonynms and making it easier to cross-reference. However, when working with a dataset, it is more convenient to use the gene symbols as these are easier to remember.
Thus, a common procedure is to replace the stable identifiers in the row names with gene symbols.
However, this is not straightforward as the gene symbols may not exist (NAs) or may be duplicated.
To assist this process, scuttle provides the uniquifyFeatureNames() function that emit gene symbols if they are unique; append the identifier, if they are duplicated; and replace the symbol with the identifier if the former is missing.
# Original row names are Ensembl IDs.
sce.ens <- ZeiselBrainData(ensembl=TRUE)
head(rownames(sce.ens)) ## [1] "ENSMUSG00000029669" "ENSMUSG00000046982" "ENSMUSG00000039735"
## [4] "ENSMUSG00000033453" "ENSMUSG00000046798" "ENSMUSG00000034009"# Replacing with guaranteed unique and non-missing symbols:
rownames(sce.ens) <- uniquifyFeatureNames(
rownames(sce.ens), rowData(sce.ens)$originalName
)
head(rownames(sce.ens)) ## [1] "Tspan12" "Tshz1" "Fnbp1l" "Adamts15" "Cldn12" "Rxfp1"data.frameThe makePerCellDF() and makePerFeatureDF() functions create data.frames from the SingleCellExperiment object.
In the makePerCellDF() case, each row of the output data.frame corresponds to a cell and each column represents the expression of a specified feature across cells, a field of the column metadata, or reduced dimensions (if any are available).
out <- makePerCellDF(sce, features="Tspan12")
colnames(out)## [1] "Tspan12" "tissue"
## [3] "group.." "total.mRNA.mol"
## [5] "well" "sex"
## [7] "age" "diameter"
## [9] "cell_id" "level1class"
## [11] "level2class" "sum"
## [13] "detected" "subsets_Mito_sum"
## [15] "subsets_Mito_detected" "subsets_Mito_percent"
## [17] "altexps_ERCC_sum" "altexps_ERCC_detected"
## [19] "altexps_ERCC_percent" "altexps_repeat_sum"
## [21] "altexps_repeat_detected" "altexps_repeat_percent"
## [23] "total" "low_lib_size"
## [25] "low_n_features" "high_subsets_Mito_percent"
## [27] "high_altexps_ERCC_percent" "discard"
## [29] "sizeFactor"In the makePerFeatureDF() case, each row of the output data.frame corresponds to a gene and each column represents the expression profile of a specified cell or the values of a row metadata field.
out2 <- makePerFeatureDF(sce, cells=c("1772063062_D05",
"1772063061_D01", "1772060240_F02", "1772062114_F05"))
colnames(out2)## [1] "1772063062_D05" "1772063061_D01" "1772060240_F02" "1772062114_F05"
## [5] "featureType"The aim is to enable the data in a SingleCellExperiment to be easily used in functions like model.matrix() or in ggplot(),
without requiring users to manually extract the desired fields from the SingleCellExperiment to construct their own data.frame.
sessionInfo()## R version 4.1.1 (2021-08-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.3 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.14-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.14-bioc/R/lib/libRlapack.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] ensembldb_2.18.0 AnnotationFilter_1.18.0
## [3] GenomicFeatures_1.46.0 AnnotationDbi_1.56.0
## [5] scuttle_1.4.0 scRNAseq_2.7.2
## [7] SingleCellExperiment_1.16.0 SummarizedExperiment_1.24.0
## [9] Biobase_2.54.0 GenomicRanges_1.46.0
## [11] GenomeInfoDb_1.30.0 IRanges_2.28.0
## [13] S4Vectors_0.32.0 BiocGenerics_0.40.0
## [15] MatrixGenerics_1.6.0 matrixStats_0.61.0
## [17] BiocStyle_2.22.0
##
## loaded via a namespace (and not attached):
## [1] ProtGenerics_1.26.0 bitops_1.0-7
## [3] bit64_4.0.5 filelock_1.0.2
## [5] progress_1.2.2 httr_1.4.2
## [7] tools_4.1.1 bslib_0.3.1
## [9] utf8_1.2.2 R6_2.5.1
## [11] lazyeval_0.2.2 DBI_1.1.1
## [13] withr_2.4.2 tidyselect_1.1.1
## [15] prettyunits_1.1.1 bit_4.0.4
## [17] curl_4.3.2 compiler_4.1.1
## [19] xml2_1.3.2 DelayedArray_0.20.0
## [21] rtracklayer_1.54.0 bookdown_0.24
## [23] sass_0.4.0 rappdirs_0.3.3
## [25] Rsamtools_2.10.0 stringr_1.4.0
## [27] digest_0.6.28 rmarkdown_2.11
## [29] XVector_0.34.0 pkgconfig_2.0.3
## [31] htmltools_0.5.2 sparseMatrixStats_1.6.0
## [33] dbplyr_2.1.1 fastmap_1.1.0
## [35] rlang_0.4.12 RSQLite_2.2.8
## [37] DelayedMatrixStats_1.16.0 shiny_1.7.1
## [39] jquerylib_0.1.4 BiocIO_1.4.0
## [41] generics_0.1.1 jsonlite_1.7.2
## [43] BiocParallel_1.28.0 dplyr_1.0.7
## [45] RCurl_1.98-1.5 magrittr_2.0.1
## [47] GenomeInfoDbData_1.2.7 Matrix_1.3-4
## [49] Rcpp_1.0.7 fansi_0.5.0
## [51] lifecycle_1.0.1 stringi_1.7.5
## [53] yaml_2.2.1 zlibbioc_1.40.0
## [55] BiocFileCache_2.2.0 AnnotationHub_3.2.0
## [57] grid_4.1.1 blob_1.2.2
## [59] parallel_4.1.1 promises_1.2.0.1
## [61] ExperimentHub_2.2.0 crayon_1.4.1
## [63] lattice_0.20-45 beachmat_2.10.0
## [65] Biostrings_2.62.0 hms_1.1.1
## [67] KEGGREST_1.34.0 knitr_1.36
## [69] pillar_1.6.4 rjson_0.2.20
## [71] biomaRt_2.50.0 XML_3.99-0.8
## [73] glue_1.4.2 BiocVersion_3.14.0
## [75] evaluate_0.14 BiocManager_1.30.16
## [77] png_0.1-7 vctrs_0.3.8
## [79] httpuv_1.6.3 purrr_0.3.4
## [81] assertthat_0.2.1 cachem_1.0.6
## [83] xfun_0.27 mime_0.12
## [85] xtable_1.8-4 restfulr_0.0.13
## [87] later_1.3.0 tibble_3.1.5
## [89] GenomicAlignments_1.30.0 memoise_2.0.0
## [91] ellipsis_0.3.2 interactiveDisplayBase_1.32.0