if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SingleCellMultiModal")library(MultiAssayExperiment)
library(SingleCellMultiModal)
library(SingleCellExperiment)CITE-seq data are a combination of two data types extracted at the same time from the same cell. First data type is scRNA-seq data, while the second one consists of about a hundread of antibody-derived tags (ADT). In particular this dataset is provided by Stoeckius et al. (2017).
The user can see the available dataset by using the default options
CITEseq(DataType="cord_blood", modes="*", dry.run=TRUE, version="1.0.0")## Dataset: cord_blood## ah_id mode file_size rdataclass rdatadateadded rdatadateremoved
## 1 EH3795 scADT_Counts 0.2 Mb matrix 2020-09-23 <NA>
## 2 EH3796 scRNAseq_Counts 22.2 Mb matrix 2020-09-23 <NA>
## 3 EH8228 coldata_scRNAseq 0.1 Mb data.frame 2023-05-17 <NA>
## 4 EH8305 scADT_clrCounts 0.8 Mb matrix 2023-07-05 <NA>Or simply by setting dry.run = FALSE it downloads the data and creates the
MultiAssayExperiment object.
In this example, we will use one of the two available datasets scADT_Counts:
mae <- CITEseq(
DataType="cord_blood", modes="*", dry.run=FALSE, version="1.0.0"
)## Warning: 'ExperimentList' contains 'data.frame' or 'DataFrame',
## potential for errors with mixed data typesmae## A MultiAssayExperiment object of 3 listed
## experiments with user-defined names and respective classes.
## Containing an ExperimentList class object of length 3:
## [1] scADT: matrix with 13 rows and 7858 columns
## [2] scADT_clr: matrix with 13 rows and 7858 columns
## [3] scRNAseq: matrix with 36280 rows and 7858 columns
## Functionality:
## experiments() - obtain the ExperimentList instance
## colData() - the primary/phenotype DataFrame
## sampleMap() - the sample coordination DataFrame
## `$`, `[`, `[[` - extract colData columns, subset, or experiment
## *Format() - convert into a long or wide DataFrame
## assays() - convert ExperimentList to a SimpleList of matrices
## exportClass() - save data to flat filesExample with actual data:
experiments(mae)## ExperimentList class object of length 3:
## [1] scADT: matrix with 13 rows and 7858 columns
## [2] scADT_clr: matrix with 13 rows and 7858 columns
## [3] scRNAseq: matrix with 36280 rows and 7858 columnsCheck row annotations:
rownames(mae)## CharacterList of length 3
## [["scADT"]] CD3 CD4 CD8 CD45RA CD56 CD16 CD10 CD11c CD14 CD19 CD34 CCR5 CCR7
## [["scADT_clr"]] CD3 CD4 CD8 CD45RA CD56 CD16 CD10 CD11c CD14 CD19 CD34 CCR5 CCR7
## [["scRNAseq"]] ERCC_ERCC-00104 HUMAN_A1BG ... MOUSE_n-R5s25 MOUSE_n-R5s31Take a peek at the sampleMap:
sampleMap(mae)## DataFrame with 23574 rows and 3 columns
## assay primary colname
## <factor> <character> <character>
## 1 scADT TACAGTGTCTCGGACG TACAGTGTCTCGGACG
## 2 scADT GTTTCTACATCATCCC GTTTCTACATCATCCC
## 3 scADT GTACGTATCCCATTTA GTACGTATCCCATTTA
## 4 scADT ATGTGTGGTCGCCATG ATGTGTGGTCGCCATG
## 5 scADT AACGTTGTCAGTTAGC AACGTTGTCAGTTAGC
## ... ... ... ...
## 23570 scRNAseq AGCGTCGAGTCAAGGC AGCGTCGAGTCAAGGC
## 23571 scRNAseq GTCGGGTAGTAGCCGA GTCGGGTAGTAGCCGA
## 23572 scRNAseq GTCGGGTAGTTCGCAT GTCGGGTAGTTCGCAT
## 23573 scRNAseq TTGCCGTGTAGATTAG TTGCCGTGTAGATTAG
## 23574 scRNAseq GGCGTGTAGTGTACTC GGCGTGTAGTGTACTCThe scRNA-seq data are accessible with the name scRNAseq, which returns a
matrix object.
head(experiments(mae)$scRNAseq)[, 1:4]## TACAGTGTCTCGGACG GTTTCTACATCATCCC GTACGTATCCCATTTA
## ERCC_ERCC-00104 0 0 0
## HUMAN_A1BG 0 0 0
## HUMAN_A1BG-AS1 0 0 0
## HUMAN_A1CF 0 0 0
## HUMAN_A2M 0 0 0
## HUMAN_A2M-AS1 0 0 0
## ATGTGTGGTCGCCATG
## ERCC_ERCC-00104 0
## HUMAN_A1BG 0
## HUMAN_A1BG-AS1 0
## HUMAN_A1CF 0
## HUMAN_A2M 0
## HUMAN_A2M-AS1 0The scADT data are accessible with the name scADT, which returns a
matrix object.
head(experiments(mae)$scADT)[, 1:4]## TACAGTGTCTCGGACG GTTTCTACATCATCCC GTACGTATCCCATTTA ATGTGTGGTCGCCATG
## CD3 36 34 49 35
## CD4 28 21 38 29
## CD8 34 41 52 47
## CD45RA 228 228 300 303
## CD56 26 18 48 36
## CD16 44 38 51 59Because of already large use of some methodologies (such as
in the SingleCellExperiment vignette or CiteFuse Vignette where the
SingleCellExperiment object is used for CITE-seq data,
we provide a function for the conversion of our CITE-seq MultiAssayExperiment
object into a SingleCellExperiment object with scRNA-seq data as counts and
scADT data as altExps.
sce <- CITEseq(DataType="cord_blood", modes="*", dry.run=FALSE, version="1.0.0",
DataClass="SingleCellExperiment")## Warning: 'ExperimentList' contains 'data.frame' or 'DataFrame',
## potential for errors with mixed data typessce## class: SingleCellExperiment
## dim: 36280 7858
## metadata(0):
## assays(1): counts
## rownames(36280): ERCC_ERCC-00104 HUMAN_A1BG ... MOUSE_n-R5s25
## MOUSE_n-R5s31
## rowData names(0):
## colnames(7858): TACAGTGTCTCGGACG GTTTCTACATCATCCC ... TTGCCGTGTAGATTAG
## GGCGTGTAGTGTACTC
## colData names(6): adt.discard mito.discard ... celltype markers
## reducedDimNames(0):
## mainExpName: NULL
## altExpNames(1): scADTsessionInfo()## R version 4.4.0 beta (2024-04-15 r86425)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.19-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
##
## 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
##
## time zone: America/New_York
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] SingleCellExperiment_1.25.1 SingleCellMultiModal_1.15.1
## [3] MultiAssayExperiment_1.29.1 SummarizedExperiment_1.33.3
## [5] Biobase_2.63.1 GenomicRanges_1.55.4
## [7] GenomeInfoDb_1.39.14 IRanges_2.37.1
## [9] S4Vectors_0.41.7 BiocGenerics_0.49.1
## [11] MatrixGenerics_1.15.1 matrixStats_1.3.0
## [13] BiocStyle_2.31.0
##
## loaded via a namespace (and not attached):
## [1] KEGGREST_1.43.0 rjson_0.2.21 xfun_0.43
## [4] bslib_0.7.0 lattice_0.22-6 vctrs_0.6.5
## [7] tools_4.4.0 generics_0.1.3 curl_5.2.1
## [10] AnnotationDbi_1.65.2 tibble_3.2.1 fansi_1.0.6
## [13] RSQLite_2.3.6 blob_1.2.4 BiocBaseUtils_1.5.1
## [16] pkgconfig_2.0.3 Matrix_1.7-0 dbplyr_2.5.0
## [19] lifecycle_1.0.4 GenomeInfoDbData_1.2.12 compiler_4.4.0
## [22] Biostrings_2.71.6 htmltools_0.5.8.1 sass_0.4.9
## [25] yaml_2.3.8 pillar_1.9.0 crayon_1.5.2
## [28] jquerylib_0.1.4 DelayedArray_0.29.9 cachem_1.0.8
## [31] magick_2.8.3 abind_1.4-5 mime_0.12
## [34] ExperimentHub_2.11.3 AnnotationHub_3.11.5 tidyselect_1.2.1
## [37] digest_0.6.35 purrr_1.0.2 dplyr_1.1.4
## [40] bookdown_0.39 BiocVersion_3.19.1 fastmap_1.1.1
## [43] grid_4.4.0 cli_3.6.2 SparseArray_1.3.5
## [46] magrittr_2.0.3 S4Arrays_1.3.7 utf8_1.2.4
## [49] withr_3.0.0 rappdirs_0.3.3 filelock_1.0.3
## [52] UCSC.utils_0.99.7 bit64_4.0.5 rmarkdown_2.26
## [55] XVector_0.43.1 httr_1.4.7 bit_4.0.5
## [58] png_0.1-8 SpatialExperiment_1.13.2 memoise_2.0.1
## [61] evaluate_0.23 knitr_1.46 BiocFileCache_2.11.2
## [64] rlang_1.1.3 Rcpp_1.0.12 glue_1.7.0
## [67] DBI_1.2.2 formatR_1.14 BiocManager_1.30.22
## [70] jsonlite_1.8.8 R6_2.5.1 zlibbioc_1.49.3Stoeckius, Marlon, Christoph Hafemeister, William Stephenson, Brian Houck-Loomis, Pratip K Chattopadhyay, Harold Swerdlow, Rahul Satija, and Peter Smibert. 2017. “Simultaneous Epitope and Transcriptome Measurement in Single Cells.” Nature Methods 14 (9): 865.