Author: Martin Morgan, Valerie Obenchain, Jim Hester, Hervé Pagès

# SummarizedExperiment for Coordinating Experimental Assays, Samples, and Regions of Interest

Martin Morgan, Valerie Obenchain, Jim Hester, Hervé Pagès

#### Revised: 5 Jan, 2023

# Contents

# 1 Introduction

The `SummarizedExperiment` class is used to store rectangular matrices of experimental results, which are commonly produced by sequencing and microarray experiments. Note that `SummarizedExperiment` can simultaneously manage several experimental results or `assays` as long as they be of the same dimensions.

Each object stores observations of one or more samples, along with additional meta-data describing both the observations (features) and samples (phenotypes).

A key aspect of the `SummarizedExperiment` class is the coordination of the meta-data and assays when subsetting. For example, if you want to exclude a given sample you can do for both the meta-data and assay in one operation, which ensures the meta-data and observed data will remain in sync. Improperly accounting for meta and observational data has resulted in a number of incorrect results and retractions so this is a very desirable property.

`SummarizedExperiment` is in many ways similar to the historical `ExpressionSet`, the main distinction being that `SummarizedExperiment` is more flexible in it’s row information, allowing both `GRanges` based as well as those described by arbitrary `DataFrame`s. This makes it ideally suited to a variety of experiments, particularly sequencing based experiments such as RNA-Seq and ChIp-Seq.

# 2 Anatomy of a `SummarizedExperiment`

The SummarizedExperiment package contains two classes: `SummarizedExperiment` and `RangedSummarizedExperiment`.

`SummarizedExperiment` is a matrix-like container where rows represent features of interest (e.g. genes, transcripts, exons, etc.) and columns represent samples. The objects contain one or more assays, each represented by a matrix-like object of numeric or other mode. The rows of a `SummarizedExperiment` object represent features of interest. Information about these features is stored in a `DataFrame` object, accessible using the function `rowData()`. Each row of the `DataFrame` provides information on the feature in the corresponding row of the `SummarizedExperiment` object. Columns of the DataFrame represent different attributes of the features of interest, e.g., gene or transcript IDs, etc.

`RangedSummarizedExperiment` is the child of the `SummarizedExperiment` class which means that all the methods on `SummarizedExperiment` also work on a `RangedSummarizedExperiment`.

The fundamental difference between the two classes is that the rows of a `RangedSummarizedExperiment` object represent genomic ranges of interest instead of a `DataFrame` of features. The `RangedSummarizedExperiment` ranges are described by a `GRanges` or a `GRangesList` object, accessible using the `rowRanges()` function.

The following graphic displays the class geometry and highlights the vertical (column) and horizontal (row) relationships.

Summarized Experiment

## 2.1 Assays

The `airway` package contains an example dataset from an RNA-Seq experiment of read counts per gene for airway smooth muscles. These data are stored in a `RangedSummarizedExperiment` object which contains 8 different experimental and assays 64,102 gene transcripts.

    library(SummarizedExperiment)
    data(airway, package="airway")
    se <- airway
    se

    ## class: RangedSummarizedExperiment
    ## dim: 63677 8
    ## metadata(1): ''
    ## assays(1): counts
    ## rownames(63677): ENSG00000000003 ENSG00000000005 ... ENSG00000273492
    ##   ENSG00000273493
    ## rowData names(10): gene_id gene_name ... seq_coord_system symbol
    ## colnames(8): SRR1039508 SRR1039509 ... SRR1039520 SRR1039521
    ## colData names(9): SampleName cell ... Sample BioSample

To retrieve the experiment data from a `SummarizedExperiment` object one can use the `assays()` accessor. An object can have multiple assay datasets each of which can be accessed using the `$` operator. The `airway` dataset contains only one assay (`counts`). Here each row represents a gene transcript and each column one of the samples.

    assays(se)$counts

| SRR1039508 | SRR1039509 | SRR1039512 | SRR1039513 | SRR1039516 | SRR1039517 | SRR1039520 | SRR1039521
--- | --- | --- | --- | --- | --- | --- | --- | ---
ENSG00000000003 | 679 | 448 | 873 | 408 | 1138 | 1047 | 770 | 572
ENSG00000000005 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0
ENSG00000000419 | 467 | 515 | 621 | 365 | 587 | 799 | 417 | 508
ENSG00000000457 | 260 | 211 | 263 | 164 | 245 | 331 | 233 | 229
ENSG00000000460 | 60 | 55 | 40 | 35 | 78 | 63 | 76 | 60
ENSG00000000938 | 0 | 0 | 2 | 0 | 1 | 0 | 0 | 0
ENSG00000000971 | 3251 | 3679 | 6177 | 4252 | 6721 | 11027 | 5176 | 7995
ENSG00000001036 | 1433 | 1062 | 1733 | 881 | 1424 | 1439 | 1359 | 1109
ENSG00000001084 | 519 | 380 | 595 | 493 | 820 | 714 | 696 | 704
ENSG00000001167 | 394 | 236 | 464 | 175 | 658 | 584 | 360 | 269

## 2.2 ‘Row’ (regions-of-interest) data

The `rowRanges()` accessor is used to view the range information for a `RangedSummarizedExperiment`. (Note if this were the parent `SummarizedExperiment` class we’d use `rowData()`). The data are stored in a `GRangesList` object, where each list element corresponds to one gene transcript and the ranges in each `GRanges` correspond to the exons in the transcript.

    rowRanges(se)

    ## GRangesList object of length 63677:
    ## $ENSG00000000003
    ## GRanges object with 17 ranges and 2 metadata columns:
    ##        seqnames            ranges strand |   exon_id       exon_name
    ##           <Rle>         <IRanges>  <Rle> | <integer>     <character>
    ##    [1]        X 99883667-99884983      - |    667145 ENSE00001459322
    ##    [2]        X 99885756-99885863      - |    667146 ENSE00000868868
    ##    [3]        X 99887482-99887565      - |    667147 ENSE00000401072
    ##    [4]        X 99887538-99887565      - |    667148 ENSE00001849132
    ##    [5]        X 99888402-99888536      - |    667149 ENSE00003554016
    ##    ...      ...               ...    ... .       ...             ...
    ##   [13]        X 99890555-99890743      - |    667156 ENSE00003512331
    ##   [14]        X 99891188-99891686      - |    667158 ENSE00001886883
    ##   [15]        X 99891605-99891803      - |    667159 ENSE00001855382
    ##   [16]        X 99891790-99892101      - |    667160 ENSE00001863395
    ##   [17]        X 99894942-99894988      - |    667161 ENSE00001828996
    ##   -------
    ##   seqinfo: 722 sequences (1 circular) from an unspecified genome
    ##
    ## ...
    ## <63676 more elements>

## 2.3 ‘Column’ (sample) data

Sample meta-data describing the samples can be accessed using `colData()`, and is a `DataFrame` that can store any number of descriptive columns for each sample row.

    colData(se)

    ## DataFrame with 8 rows and 9 columns
    ##            SampleName     cell      dex    albut        Run avgLength
    ##              <factor> <factor> <factor> <factor>   <factor> <integer>
    ## SRR1039508 GSM1275862  N61311     untrt    untrt SRR1039508       126
    ## SRR1039509 GSM1275863  N61311     trt      untrt SRR1039509       126
    ## SRR1039512 GSM1275866  N052611    untrt    untrt SRR1039512       126
    ## SRR1039513 GSM1275867  N052611    trt      untrt SRR1039513        87
    ## SRR1039516 GSM1275870  N080611    untrt    untrt SRR1039516       120
    ## SRR1039517 GSM1275871  N080611    trt      untrt SRR1039517       126
    ## SRR1039520 GSM1275874  N061011    untrt    untrt SRR1039520       101
    ## SRR1039521 GSM1275875  N061011    trt      untrt SRR1039521        98
    ##            Experiment    Sample    BioSample
    ##              <factor>  <factor>     <factor>
    ## SRR1039508  SRX384345 SRS508568 SAMN02422669
    ## SRR1039509  SRX384346 SRS508567 SAMN02422675
    ## SRR1039512  SRX384349 SRS508571 SAMN02422678
    ## SRR1039513  SRX384350 SRS508572 SAMN02422670
    ## SRR1039516  SRX384353 SRS508575 SAMN02422682
    ## SRR1039517  SRX384354 SRS508576 SAMN02422673
    ## SRR1039520  SRX384357 SRS508579 SAMN02422683
    ## SRR1039521  SRX384358 SRS508580 SAMN02422677

This sample metadata can be accessed using the `$` accessor which makes it easy to subset the entire object by a given phenotype.

    # subset for only those samples treated with dexamethasone
    se[, se$dex == "trt"]

    ## class: RangedSummarizedExperiment
    ## dim: 63677 4
    ## metadata(1): ''
    ## assays(1): counts
    ## rownames(63677): ENSG00000000003 ENSG00000000005 ... ENSG00000273492
    ##   ENSG00000273493
    ## rowData names(10): gene_id gene_name ... seq_coord_system symbol
    ## colnames(4): SRR1039509 SRR1039513 SRR1039517 SRR1039521
    ## colData names(9): SampleName cell ... Sample BioSample

## 2.4 Experiment-wide metadata

Meta-data describing the experimental methods and publication references can be accessed using `metadata()`.

    metadata(se)

    ## [[1]]
    ## Experiment data
    ##   Experimenter name: Himes BE
    ##   Laboratory: NA
    ##   Contact information:
    ##   Title: RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells.
    ##   URL: http://www.ncbi.nlm.nih.gov/pubmed/24926665
    ##   PMIDs: 24926665
    ##
    ##   Abstract: A 226 word abstract is available. Use 'abstract' method.

Note that `metadata()` is just a simple list, so it is appropriate for any experiment wide metadata the user wishes to save, such as storing model formulas.

    metadata(se)$formula <- counts ~ dex + albut

    metadata(se)

    ## [[1]]
    ## Experiment data
    ##   Experimenter name: Himes BE
    ##   Laboratory: NA
    ##   Contact information:
    ##   Title: RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells.
    ##   URL: http://www.ncbi.nlm.nih.gov/pubmed/24926665
    ##   PMIDs: 24926665
    ##
    ##   Abstract: A 226 word abstract is available. Use 'abstract' method.
    ##
    ## $formula
    ## counts ~ dex + albut

# 3 Constructing a `SummarizedExperiment`

Often, `SummarizedExperiment` or `RangedSummarizedExperiment` objects are returned by functions written by other packages. However it is possible to create them by hand with a call to the `SummarizedExperiment()` constructor.

Constructing a `RangedSummarizedExperiment` with a `GRanges` as the rowRanges argument:

    nrows <- 200
    ncols <- 6
    counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
    rowRanges <- GRanges(rep(c("chr1", "chr2"), c(50, 150)),
                         IRanges(floor(runif(200, 1e5, 1e6)), width=100),
                         strand=sample(c("+", "-"), 200, TRUE),
                         feature_id=sprintf("ID%03d", 1:200))
    colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
                         row.names=LETTERS[1:6])

    SummarizedExperiment(assays=list(counts=counts),
                         rowRanges=rowRanges, colData=colData)

    ## class: RangedSummarizedExperiment
    ## dim: 200 6
    ## metadata(0):
    ## assays(1): counts
    ## rownames: NULL
    ## rowData names(1): feature_id
    ## colnames(6): A B ... E F
    ## colData names(1): Treatment

A `SummarizedExperiment` can be constructed with or without supplying a `DataFrame` for the rowData argument:

    SummarizedExperiment(assays=list(counts=counts), colData=colData)

    ## class: SummarizedExperiment
    ## dim: 200 6
    ## metadata(0):
    ## assays(1): counts
    ## rownames: NULL
    ## rowData names(0):
    ## colnames(6): A B ... E F
    ## colData names(1): Treatment

# 4 Top-level dimnames vs assay-level dimnames

In addition to the dimnames that are set on a `SummarizedExperiment` object itself, the individual assays that are stored in the object can have their own dimnames or not:

    a1 <- matrix(runif(24), ncol=6, dimnames=list(letters[1:4], LETTERS[1:6]))
    a2 <- matrix(rpois(24, 0.8), ncol=6)
    a3 <- matrix(101:124, ncol=6, dimnames=list(NULL, LETTERS[1:6]))
    se3 <- SummarizedExperiment(SimpleList(a1, a2, a3))

The dimnames of the `SummarizedExperiment` object (top-level dimnames):

    dimnames(se3)

    ## [[1]]
    ## [1] "a" "b" "c" "d"
    ##
    ## [[2]]
    ## [1] "A" "B" "C" "D" "E" "F"

When extracting assays from the object, the top-level dimnames are put on them by default:

    assay(se3, 2)  # this is 'a2', but with the top-level dimnames on it

    ##   A B C D E F
    ## a 0 1 1 0 1 2
    ## b 1 1 0 0 1 0
    ## c 2 3 1 0 0 1
    ## d 0 3 0 0 2 1

    assay(se3, 3)  # this is 'a3', but with the top-level dimnames on it

    ##     A   B   C   D   E   F
    ## a 101 105 109 113 117 121
    ## b 102 106 110 114 118 122
    ## c 103 107 111 115 119 123
    ## d 104 108 112 116 120 124

However if using `withDimnames=FALSE` then the assays are returned as-is, i.e. with their original dimnames (this is how they are stored in the `SummarizedExperiment` object):

    assay(se3, 2, withDimnames=FALSE)  # identical to 'a2'

    ##      [,1] [,2] [,3] [,4] [,5] [,6]
    ## [1,]    0    1    1    0    1    2
    ## [2,]    1    1    0    0    1    0
    ## [3,]    2    3    1    0    0    1
    ## [4,]    0    3    0    0    2    1

    assay(se3, 3, withDimnames=FALSE)  # identical to 'a3'

    ##        A   B   C   D   E   F
    ## [1,] 101 105 109 113 117 121
    ## [2,] 102 106 110 114 118 122
    ## [3,] 103 107 111 115 119 123
    ## [4,] 104 108 112 116 120 124

    rownames(se3) <- strrep(letters[1:4], 3)

    dimnames(se3)

    ## [[1]]
    ## [1] "aaa" "bbb" "ccc" "ddd"
    ##
    ## [[2]]
    ## [1] "A" "B" "C" "D" "E" "F"

    assay(se3, 1)  # this is 'a1', but with the top-level dimnames on it

    ##             A         B         C         D         E          F
    ## aaa 0.2992699 0.3148945 0.6513318 0.1739945 0.8229840 0.11121846
    ## bbb 0.2226603 0.6964976 0.7666522 0.5122314 0.1015872 0.79819591
    ## ccc 0.1624147 0.3756149 0.4628455 0.3815897 0.6299210 0.39517623
    ## ddd 0.4444912 0.3988797 0.2469224 0.2034942 0.5330762 0.03742089

    assay(se3, 1, withDimnames=FALSE)  # identical to 'a1'

    ##           A         B         C         D         E          F
    ## a 0.2992699 0.3148945 0.6513318 0.1739945 0.8229840 0.11121846
    ## b 0.2226603 0.6964976 0.7666522 0.5122314 0.1015872 0.79819591
    ## c 0.1624147 0.3756149 0.4628455 0.3815897 0.6299210 0.39517623
    ## d 0.4444912 0.3988797 0.2469224 0.2034942 0.5330762 0.03742089

# 5 Common operations on `SummarizedExperiment`

## 5.1 Subsetting

- `[` Performs two dimensional subsetting, just like subsetting a matrix or data frame.

    # subset the first five transcripts and first three samples
    se[1:5, 1:3]

    ## class: RangedSummarizedExperiment
    ## dim: 5 3
    ## metadata(2): '' formula
    ## assays(1): counts
    ## rownames(5): ENSG00000000003 ENSG00000000005 ENSG00000000419
    ##   ENSG00000000457 ENSG00000000460
    ## rowData names(10): gene_id gene_name ... seq_coord_system symbol
    ## colnames(3): SRR1039508 SRR1039509 SRR1039512
    ## colData names(9): SampleName cell ... Sample BioSample

- `$` operates on `colData()` columns, for easy sample extraction.

    se[, se$cell == "N61311"]

    ## class: RangedSummarizedExperiment
    ## dim: 63677 2
    ## metadata(2): '' formula
    ## assays(1): counts
    ## rownames(63677): ENSG00000000003 ENSG00000000005 ... ENSG00000273492
    ##   ENSG00000273493
    ## rowData names(10): gene_id gene_name ... seq_coord_system symbol
    ## colnames(2): SRR1039508 SRR1039509
    ## colData names(9): SampleName cell ... Sample BioSample

## 5.2 Getters and setters

- `rowRanges()` / (`rowData()`), `colData()`, `metadata()`

    counts <- matrix(1:15, 5, 3, dimnames=list(LETTERS[1:5], LETTERS[1:3]))

    dates <- SummarizedExperiment(assays=list(counts=counts),
                                  rowData=DataFrame(month=month.name[1:5], day=1:5))

    # Subset all January assays
    dates[rowData(dates)$month == "January", ]

    ## class: SummarizedExperiment
    ## dim: 1 3
    ## metadata(0):
    ## assays(1): counts
    ## rownames(1): A
    ## rowData names(2): month day
    ## colnames(3): A B C
    ## colData names(0):

- `assay()` versus `assays()` There are two accessor functions for extracting the assay data from a `SummarizedExperiment` object. `assays()` operates on the entire list of assay data as a whole, while `assay()` operates on only one assay at a time. `assay(x, i)` is simply a convenience function which is equivalent to `assays(x)[[i]]`.

    assays(se)

    ## List of length 1
    ## names(1): counts

    assays(se)[[1]][1:5, 1:5]

    ##                 SRR1039508 SRR1039509 SRR1039512 SRR1039513 SRR1039516
    ## ENSG00000000003        679        448        873        408       1138
    ## ENSG00000000005          0          0          0          0          0
    ## ENSG00000000419        467        515        621        365        587
    ## ENSG00000000457        260        211        263        164        245
    ## ENSG00000000460         60         55         40         35         78

    # assay defaults to the first assay if no i is given
    assay(se)[1:5, 1:5]

    ##                 SRR1039508 SRR1039509 SRR1039512 SRR1039513 SRR1039516
    ## ENSG00000000003        679        448        873        408       1138
    ## ENSG00000000005          0          0          0          0          0
    ## ENSG00000000419        467        515        621        365        587
    ## ENSG00000000457        260        211        263        164        245
    ## ENSG00000000460         60         55         40         35         78

    assay(se, 1)[1:5, 1:5]

    ##                 SRR1039508 SRR1039509 SRR1039512 SRR1039513 SRR1039516
    ## ENSG00000000003        679        448        873        408       1138
    ## ENSG00000000005          0          0          0          0          0
    ## ENSG00000000419        467        515        621        365        587
    ## ENSG00000000457        260        211        263        164        245
    ## ENSG00000000460         60         55         40         35         78

## 5.3 Range-based operations

- `subsetByOverlaps()` `SummarizedExperiment` objects support all of the `findOverlaps()` methods and associated functions. This includes `subsetByOverlaps()`, which makes it easy to subset a `SummarizedExperiment` object by an interval.

    # Subset for only rows which are in the interval 100,000 to 110,000 of
    # chromosome 1
    roi <- GRanges(seqnames="1", ranges=100000:1100000)
    subsetByOverlaps(se, roi)

    ## class: RangedSummarizedExperiment
    ## dim: 74 8
    ## metadata(2): '' formula
    ## assays(1): counts
    ## rownames(74): ENSG00000131591 ENSG00000177757 ... ENSG00000272512
    ##   ENSG00000273443
    ## rowData names(10): gene_id gene_name ... seq_coord_system symbol
    ## colnames(8): SRR1039508 SRR1039509 ... SRR1039520 SRR1039521
    ## colData names(9): SampleName cell ... Sample BioSample

# 6 Interactive visualization

The iSEE package provides functions for creating an interactive user interface based on the shiny package for exploring data stored in `SummarizedExperiment` objects. Information stored in standard components of `SummarizedExperiment` objects – including assay data, and row and column metadata – are automatically detected and used to populate the interactive multi-panel user interface. Particular attention is given to the SingleCellExperiment extension of the `SummarizedExperiment` class, with visualization of dimensionality reduction results.

Extensions to the iSEE package provide support for more context-dependent functionality:

- iSEEde provides additional panels that facilitate the interactive visualization of differential expression results, including the `DESeqDataSet` extension of `SummarizedExperiment` implemented in DESeq2.
- iSEEpathways provides additional panels for the interactive visualization of pathway analysis results.
- iSEEhub provides functionality to import data sets stored in the Bioconductor ExperimentHub.
- iSEEhub provides functionality to import data sets from custom sources (local and remote).

# 7 Session information

    sessionInfo()

    ## R Under development (unstable) (2025-10-20 r88955)
    ## Platform: x86_64-pc-linux-gnu
    ## Running under: Ubuntu 24.04.3 LTS
    ##
    ## Matrix products: default
    ## BLAS:   /home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so
    ## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0  LAPACK version 3.12.0
    ##
    ## 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] testthat_3.2.3              SummarizedExperiment_1.41.0
    ##  [3] Biobase_2.71.0              GenomicRanges_1.63.0
    ##  [5] Seqinfo_1.1.0               IRanges_2.45.0
    ##  [7] S4Vectors_0.49.0            BiocGenerics_0.57.0
    ##  [9] generics_0.1.4              MatrixGenerics_1.23.0
    ## [11] matrixStats_1.5.0           BiocStyle_2.39.0
    ##
    ## loaded via a namespace (and not attached):
    ##  [1] Matrix_1.7-4        jsonlite_2.0.0      compiler_4.6.0
    ##  [4] BiocManager_1.30.26 brio_1.1.5          jquerylib_0.1.4
    ##  [7] yaml_2.3.10         fastmap_1.2.0       lattice_0.22-7
    ## [10] R6_2.6.1            XVector_0.51.0      S4Arrays_1.11.0
    ## [13] knitr_1.50          DelayedArray_0.37.0 bookdown_0.45
    ## [16] desc_1.4.3          rprojroot_2.1.1     pillar_1.11.1
    ## [19] bslib_0.9.0         rlang_1.1.6         cachem_1.1.0
    ## [22] xfun_0.54           sass_0.4.10         pkgload_1.4.1
    ## [25] SparseArray_1.11.1  cli_3.6.5           withr_3.0.2
    ## [28] magrittr_2.0.4      digest_0.6.37       grid_4.6.0
    ## [31] lifecycle_1.0.4     vctrs_0.6.5         waldo_0.6.2
    ## [34] glue_1.8.0          evaluate_1.0.5      abind_1.4-8
    ## [37] rmarkdown_2.30      tools_4.6.0         htmltools_0.5.8.1