# Working with aggregate functions

Giulia Pais1*

1San Raffaele Telethon Institute for Gene Therapy - SR-Tiget, Via Olgettina 60, 20132 Milano - Italia

* giuliapais1@gmail.com, calabria.andrea@hsr.it

#### 28 October 2021

#### Package

ISAnalytics 1.4.1

# 1 Introduction

In this vignette we’re going to explain in detail how to use functions of the aggregate family, namely:

1. `aggregate_metadata()`
2. `aggregate_values_by_key()`

# 2 Installation and options

`ISAnalytics` can be installed quickly in different ways:

- You can install it via Bioconductor
- You can install it via GitHub using the package `devtools`

There are always 2 versions of the package active:

- `RELEASE` is the latest stable version
- `DEVEL` is the development version, it is the most up-to-date version where all new features are introduced

## 2.1 Installation from bioconductor

RELEASE version:

    if (!requireNamespace("BiocManager", quietly = TRUE))
        install.packages("BiocManager")
    BiocManager::install("ISAnalytics")

DEVEL version:

    if (!requireNamespace("BiocManager", quietly = TRUE))
        install.packages("BiocManager")

    # The following initializes usage of Bioc devel
    BiocManager::install(version='devel')

    BiocManager::install("ISAnalytics")

## 2.2 Installation from GitHub

RELEASE:

    if (!require(devtools)) {
      install.packages("devtools")
    }
    devtools::install_github("calabrialab/ISAnalytics",
                             ref = "RELEASE_3_14",
                             dependencies = TRUE,
                             build_vignettes = TRUE)

DEVEL:

    if (!require(devtools)) {
      install.packages("devtools")
    }
    devtools::install_github("calabrialab/ISAnalytics",
                             ref = "master",
                             dependencies = TRUE,
                             build_vignettes = TRUE)

## 2.3 Setting options

`ISAnalytics` has a verbose option that allows some functions to print additional information to the console while they’re executing. To disable this feature do:

    # DISABLE
    options("ISAnalytics.verbose" = FALSE)

    # ENABLE
    options("ISAnalytics.verbose" = TRUE)

Some functions also produce report in a user-friendly HTML format, to set this feature:

    # DISABLE HTML REPORTS
    options("ISAnalytics.reports" = FALSE)

    # ENABLE HTML REPORTS
    options("ISAnalytics.reports" = TRUE)

# 3 Aggregating metadata

We refer to information contained in the association file as “metadata”: sometimes it’s useful to obtain collective information based on a certain group of variables we’re interested in. The function `aggregate_metadata()` does just that: according to the grouping variables, meaning the names of the columns in the association file to perform a `group_by` operation with,it creates a summary. You can fully customize the summary by providing a “function table” that tells the function which operation should be applied to which column and what name to give to the output column. A default is already supplied:

    #> Loading required package: magrittr
    #> # A tibble: 12 × 4
    #>    Column               Function  Args  Output_colname
    #>    <chr>                <list>    <lgl> <chr>
    #>  1 FusionPrimerPCRDate  <formula> NA    {.col}_min
    #>  2 LinearPCRDate        <formula> NA    {.col}_min
    #>  3 VCN                  <formula> NA    {.col}_avg
    #>  4 ng DNA corrected     <formula> NA    {.col}_avg
    #>  5 Kapa                 <formula> NA    {.col}_avg
    #>  6 ng DNA corrected     <formula> NA    {.col}_sum
    #>  7 ulForPool            <formula> NA    {.col}_sum
    #>  8 BARCODE_MUX          <formula> NA    {.col}_sum
    #>  9 TRIMMING_FINAL_LTRLC <formula> NA    {.col}_sum
    #> 10 LV_MAPPED            <formula> NA    {.col}_sum
    #> 11 BWA_MAPPED_OVERALL   <formula> NA    {.col}_sum
    #> 12 ISS_MAPPED_PP        <formula> NA    {.col}_sum

You can either provide purrr-style lambdas (as given in the example above), or simply specify the name of the function and additional parameters as a list in a separated column. If you choose to provide your own table you should maintain the column names for the function to work properly. For more details on this take a look at the function documentation `?default_meta_agg`.

## 3.1 Typical workflow

1. Import the association file via `import_assocition_file()`. If you need more information on import function please view the vignette “How to use import functions”: `vignette("how_to_import_functions", package="ISAnalytics")`.
2. Perform aggregation

    data("association_file", package = "ISAnalytics")
    aggregated_meta <- aggregate_metadata(association_file = association_file)

    #> # A tibble: 20 × 16
    #>    SubjectID CellMarker Tissue TimePoint FusionPrimerPCRDate_m… LinearPCRDate_m…
    #>    <chr>     <chr>      <chr>  <chr>     <date>                 <date>
    #>  1 PT001     MNC        BM     0030      2016-11-03             NA
    #>  2 PT001     MNC        BM     0060      2016-11-03             NA
    #>  3 PT001     MNC        BM     0090      2016-11-03             NA
    #>  4 PT001     MNC        BM     0180      2016-11-03             NA
    #>  5 PT001     MNC        BM     0360      2017-04-21             NA
    #>  6 PT001     MNC        PB     0030      2016-11-03             NA
    #>  7 PT001     MNC        PB     0060      2016-11-03             NA
    #>  8 PT001     MNC        PB     0090      2016-11-03             NA
    #>  9 PT001     MNC        PB     0180      2016-11-03             NA
    #> 10 PT001     MNC        PB     0360      2017-04-21             NA
    #> 11 PT002     MNC        BM     0030      2017-04-21             NA
    #> 12 PT002     MNC        BM     0060      2017-05-05             NA
    #> 13 PT002     MNC        BM     0090      2017-05-05             NA
    #> 14 PT002     MNC        BM     0180      2017-05-16             NA
    #> 15 PT002     MNC        BM     0360      2018-03-12             NA
    #> 16 PT002     MNC        PB     0030      2017-04-21             NA
    #> 17 PT002     MNC        PB     0060      2017-05-05             NA
    #> 18 PT002     MNC        PB     0090      2017-05-05             NA
    #> 19 PT002     MNC        PB     0180      2017-05-05             NA
    #> 20 PT002     MNC        PB     0360      2018-03-12             NA
    #> # … with 10 more variables: VCN_avg <dbl>, ng DNA corrected_avg <dbl>,
    #> #   Kapa_avg <dbl>, ng DNA corrected_sum <dbl>, ulForPool_sum <dbl>,
    #> #   BARCODE_MUX_sum <int>, TRIMMING_FINAL_LTRLC_sum <int>, LV_MAPPED_sum <int>,
    #> #   BWA_MAPPED_OVERALL_sum <int>, ISS_MAPPED_PP_sum <int>

# 4 Aggregation of values by key

`ISAnalytics` contains useful functions to aggregate the values contained in your imported matrices based on a key, aka a single column or a combination of columns contained in the association file that are related to the samples.

## 4.1 Typical workflow

1. Import your association file
2. Import integration matrices via `import_parallel_Vispa2Matrices()`
3. Perform aggregation

    data("integration_matrices", package = "ISAnalytics")
    data("association_file", package = "ISAnalytics")
    aggreg <- aggregate_values_by_key(
      x = integration_matrices,
      association_file = association_file,
      value_cols = c("seqCount", "fragmentEstimate")
    )

    #> # A tibble: 1,074 × 11
    #>    chr   integration_locus strand GeneName GeneStrand SubjectID CellMarker
    #>    <chr>             <dbl> <chr>  <chr>    <chr>      <chr>     <chr>
    #>  1 1               8464757 -      RERE     -          PT001     MNC
    #>  2 1               8464757 -      RERE     -          PT001     MNC
    #>  3 1               8607357 +      RERE     -          PT001     MNC
    #>  4 1               8607357 +      RERE     -          PT001     MNC
    #>  5 1               8607357 +      RERE     -          PT001     MNC
    #>  6 1               8607362 -      RERE     -          PT001     MNC
    #>  7 1               8850362 +      RERE     -          PT002     MNC
    #>  8 1              11339120 +      UBIAD1   +          PT001     MNC
    #>  9 1              11339120 +      UBIAD1   +          PT001     MNC
    #> 10 1              11339120 +      UBIAD1   +          PT001     MNC
    #>    Tissue TimePoint seqCount_sum fragmentEstimate_sum
    #>    <chr>  <chr>            <dbl>                <dbl>
    #>  1 BM     0030               542                 3.01
    #>  2 BM     0060                 1                 1.00
    #>  3 BM     0060                 1                 1.00
    #>  4 BM     0180              1096                 5.01
    #>  5 BM     0360               330                34.1
    #>  6 BM     0180              1702                 4.01
    #>  7 BM     0360               562                 3.01
    #>  8 BM     0060              1605                 8.03
    #>  9 PB     0060                 1                 1.00
    #> 10 PB     0180                 1                 1.00
    #> # … with 1,064 more rows

The function `aggregate_values_by_key` can perform the aggregation both on the list of matrices and a single matrix.

### 4.1.1 Changing parameters to obtain different results

The function has several different parameters that have default values that can be changed according to user preference.

1. Changing the `key` value
   You can change the value of the parameter key as you see fit. This parameter should contain one or multiple columns of the association file that you want to include in the grouping when performing the aggregation. The default value is set to `c("SubjectID", "CellMarker", "Tissue", "TimePoint")` (same default key as the `aggregate_metadata` function).

    agg1 <- aggregate_values_by_key(
        x = integration_matrices,
        association_file = association_file,
        key = c("SubjectID", "ProjectID"),
        value_cols = c("seqCount", "fragmentEstimate")
    )

    #> # A tibble: 577 × 9
    #>    chr   integration_locus strand GeneName GeneStrand SubjectID ProjectID
    #>    <chr>             <dbl> <chr>  <chr>    <chr>      <chr>     <chr>
    #>  1 1               8464757 -      RERE     -          PT001     PJ01
    #>  2 1               8607357 +      RERE     -          PT001     PJ01
    #>  3 1               8607362 -      RERE     -          PT001     PJ01
    #>  4 1               8850362 +      RERE     -          PT002     PJ01
    #>  5 1              11339120 +      UBIAD1   +          PT001     PJ01
    #>  6 1              12341466 -      VPS13D   +          PT002     PJ01
    #>  7 1              14034054 -      PRDM2    +          PT002     PJ01
    #>  8 1              16186297 -      SPEN     +          PT001     PJ01
    #>  9 1              16602483 +      FBXO42   -          PT001     PJ01
    #> 10 1              16602483 +      FBXO42   -          PT002     PJ01
    #>    seqCount_sum fragmentEstimate_sum
    #>           <dbl>                <dbl>
    #>  1          543                 4.01
    #>  2         1427                40.1
    #>  3         1702                 4.01
    #>  4          562                 3.01
    #>  5         1607                10.0
    #>  6         1843                 8.05
    #>  7         1938                 3.01
    #>  8         3494                16.1
    #>  9         2947                 9.04
    #> 10           30                 2.00
    #> # … with 567 more rows

2. Changing the `lambda` value
   The `lambda` parameter indicates the function(s) to be applied to the values for aggregation. `lambda` must be a named list of either functions or purrr-style lambdas: if you would like to specify additional parameters to the function the second option is recommended. The only important note on functions is that they should perform some kind of aggregation on numeric values: this means in practical terms they need to accept a vector of numeric/integer values as input and produce a SINGLE value as output. Valid options for this purpose might be: `sum`, `mean`, `median`, `min`, `max` and so on.

    agg2 <- aggregate_values_by_key(
        x = integration_matrices,
        association_file = association_file,
        key = "SubjectID",
        lambda = list(mean = ~ mean(.x, na.rm = TRUE)),
        value_cols = c("seqCount", "fragmentEstimate")
    )

    #> # A tibble: 577 × 8
    #>    chr   integration_locus strand GeneName GeneStrand SubjectID seqCount_mean
    #>    <chr>             <dbl> <chr>  <chr>    <chr>      <chr>             <dbl>
    #>  1 1               8464757 -      RERE     -          PT001              272.
    #>  2 1               8607357 +      RERE     -          PT001              285.
    #>  3 1               8607362 -      RERE     -          PT001              851
    #>  4 1               8850362 +      RERE     -          PT002              562
    #>  5 1              11339120 +      UBIAD1   +          PT001              321.
    #>  6 1              12341466 -      VPS13D   +          PT002             1843
    #>  7 1              14034054 -      PRDM2    +          PT002             1938
    #>  8 1              16186297 -      SPEN     +          PT001              699.
    #>  9 1              16602483 +      FBXO42   -          PT001              982.
    #> 10 1              16602483 +      FBXO42   -          PT002               30
    #>    fragmentEstimate_mean
    #>                    <dbl>
    #>  1                  2.01
    #>  2                  8.02
    #>  3                  2.01
    #>  4                  3.01
    #>  5                  2.01
    #>  6                  8.05
    #>  7                  3.01
    #>  8                  3.22
    #>  9                  3.01
    #> 10                  2.00
    #> # … with 567 more rows

Note that, when specifying purrr-style lambdas (formulas), the first parameter needs to be set to `.x`, other parameters can be set as usual.

You can also use in `lambda` functions that produce data frames or lists. In this case all variables from the produced data frame will be included in the final data frame. For example:

    agg3 <- aggregate_values_by_key(
        x = integration_matrices,
        association_file = association_file,
        key = "SubjectID",
        lambda = list(describe = ~ list(psych::describe(.x))),
        value_cols = c("seqCount", "fragmentEstimate")
    )

    #> # A tibble: 577 × 8
    #>    chr   integration_locus strand GeneName GeneStrand SubjectID
    #>    <chr>             <dbl> <chr>  <chr>    <chr>      <chr>
    #>  1 1               8464757 -      RERE     -          PT001
    #>  2 1               8607357 +      RERE     -          PT001
    #>  3 1               8607362 -      RERE     -          PT001
    #>  4 1               8850362 +      RERE     -          PT002
    #>  5 1              11339120 +      UBIAD1   +          PT001
    #>  6 1              12341466 -      VPS13D   +          PT002
    #>  7 1              14034054 -      PRDM2    +          PT002
    #>  8 1              16186297 -      SPEN     +          PT001
    #>  9 1              16602483 +      FBXO42   -          PT001
    #> 10 1              16602483 +      FBXO42   -          PT002
    #>    seqCount_describe fragmentEstimate_describe
    #>    <list>            <list>
    #>  1 <psych [1 × 13]>  <psych [1 × 13]>
    #>  2 <psych [1 × 13]>  <psych [1 × 13]>
    #>  3 <psych [1 × 13]>  <psych [1 × 13]>
    #>  4 <psych [1 × 13]>  <psych [1 × 13]>
    #>  5 <psych [1 × 13]>  <psych [1 × 13]>
    #>  6 <psych [1 × 13]>  <psych [1 × 13]>
    #>  7 <psych [1 × 13]>  <psych [1 × 13]>
    #>  8 <psych [1 × 13]>  <psych [1 × 13]>
    #>  9 <psych [1 × 13]>  <psych [1 × 13]>
    #> 10 <psych [1 × 13]>  <psych [1 × 13]>
    #> # … with 567 more rows

3. Changing the `value_cols` value
   The `value_cols` parameter tells the function on which numeric columns of x the functions should be applied. Note that every function contained in `lambda` will be applied to every column in `value_cols`: resulting columns will be named as “original name_function applied”.

    agg4 <- aggregate_values_by_key(
        x = integration_matrices,
        association_file = association_file,
        key = "SubjectID",
        lambda = list(sum = sum, mean = mean),
        value_cols = c("seqCount", "fragmentEstimate")
    )

    #> # A tibble: 577 × 10
    #>    chr   integration_locus strand GeneName GeneStrand SubjectID seqCount_sum
    #>    <chr>             <dbl> <chr>  <chr>    <chr>      <chr>            <dbl>
    #>  1 1               8464757 -      RERE     -          PT001              543
    #>  2 1               8607357 +      RERE     -          PT001             1427
    #>  3 1               8607362 -      RERE     -          PT001             1702
    #>  4 1               8850362 +      RERE     -          PT002              562
    #>  5 1              11339120 +      UBIAD1   +          PT001             1607
    #>  6 1              12341466 -      VPS13D   +          PT002             1843
    #>  7 1              14034054 -      PRDM2    +          PT002             1938
    #>  8 1              16186297 -      SPEN     +          PT001             3494
    #>  9 1              16602483 +      FBXO42   -          PT001             2947
    #> 10 1              16602483 +      FBXO42   -          PT002               30
    #>    seqCount_mean fragmentEstimate_sum fragmentEstimate_mean
    #>            <dbl>                <dbl>                 <dbl>
    #>  1          272.                 4.01                  2.01
    #>  2          285.                40.1                   8.02
    #>  3          851                  4.01                  2.01
    #>  4          562                  3.01                  3.01
    #>  5          321.                10.0                   2.01
    #>  6         1843                  8.05                  8.05
    #>  7         1938                  3.01                  3.01
    #>  8          699.                16.1                   3.22
    #>  9          982.                 9.04                  3.01
    #> 10           30                  2.00                  2.00
    #> # … with 567 more rows

4. Changing the `group` value
   The `group` parameter should contain all other variables to include in the grouping besides `key`. By default this contains `c("chr", "integration_locus","strand", "GeneName", "GeneStrand")`. You can change this grouping as you see fit, if you don’t want to add any other variable to the key, just set it to `NULL`.

    agg5 <- aggregate_values_by_key(
        x = integration_matrices,
        association_file = association_file,
        key = "SubjectID",
        lambda = list(sum = sum, mean = mean),
        group = c(mandatory_IS_vars()),
        value_cols = c("seqCount", "fragmentEstimate")
    )

    #> # A tibble: 577 × 8
    #>    chr   integration_locus strand SubjectID seqCount_sum seqCount_mean
    #>    <chr>             <dbl> <chr>  <chr>            <dbl>         <dbl>
    #>  1 1               8464757 -      PT001              543          272.
    #>  2 1               8607357 +      PT001             1427          285.
    #>  3 1               8607362 -      PT001             1702          851
    #>  4 1               8850362 +      PT002              562          562
    #>  5 1              11339120 +      PT001             1607          321.
    #>  6 1              12341466 -      PT002             1843         1843
    #>  7 1              14034054 -      PT002             1938         1938
    #>  8 1              16186297 -      PT001             3494          699.
    #>  9 1              16602483 +      PT001             2947          982.
    #> 10 1              16602483 +      PT002               30           30
    #>    fragmentEstimate_sum fragmentEstimate_mean
    #>                   <dbl>                 <dbl>
    #>  1                 4.01                  2.01
    #>  2                40.1                   8.02
    #>  3                 4.01                  2.01
    #>  4                 3.01                  3.01
    #>  5                10.0                   2.01
    #>  6                 8.05                  8.05
    #>  7                 3.01                  3.01
    #>  8                16.1                   3.22
    #>  9                 9.04                  3.01
    #> 10                 2.00                  2.00
    #> # … with 567 more rows

# 5 Reproducibility

`R` session information.

    #> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
    #>  setting  value
    #>  version  R version 4.1.1 (2021-08-10)
    #>  os       Ubuntu 20.04.3 LTS
    #>  system   x86_64, linux-gnu
    #>  ui       X11
    #>  language (EN)
    #>  collate  C
    #>  ctype    en_US.UTF-8
    #>  tz       America/New_York
    #>  date     2021-10-28
    #>
    #> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
    #>  package      * version date       lib source
    #>  assertthat     0.2.1   2019-03-21 [2] CRAN (R 4.1.1)
    #>  BiocManager    1.30.16 2021-06-15 [2] CRAN (R 4.1.1)
    #>  BiocParallel   1.28.0  2021-10-28 [2] Bioconductor
    #>  BiocStyle    * 2.22.0  2021-10-28 [2] Bioconductor
    #>  bookdown       0.24    2021-09-02 [2] CRAN (R 4.1.1)
    #>  bslib          0.3.1   2021-10-06 [2] CRAN (R 4.1.1)
    #>  cli            3.1.0   2021-10-27 [2] CRAN (R 4.1.1)
    #>  colorspace     2.0-2   2021-06-24 [2] CRAN (R 4.1.1)
    #>  crayon         1.4.1   2021-02-08 [2] CRAN (R 4.1.1)
    #>  data.table     1.14.2  2021-09-27 [2] CRAN (R 4.1.1)
    #>  DBI            1.1.1   2021-01-15 [2] CRAN (R 4.1.1)
    #>  digest         0.6.28  2021-09-23 [2] CRAN (R 4.1.1)
    #>  dplyr          1.0.7   2021-06-18 [2] CRAN (R 4.1.1)
    #>  ellipsis       0.3.2   2021-04-29 [2] CRAN (R 4.1.1)
    #>  evaluate       0.14    2019-05-28 [2] CRAN (R 4.1.1)
    #>  fansi          0.5.0   2021-05-25 [2] CRAN (R 4.1.1)
    #>  fastmap        1.1.0   2021-01-25 [2] CRAN (R 4.1.1)
    #>  fs             1.5.0   2020-07-31 [2] CRAN (R 4.1.1)
    #>  generics       0.1.1   2021-10-25 [2] CRAN (R 4.1.1)
    #>  ggplot2        3.3.5   2021-06-25 [2] CRAN (R 4.1.1)
    #>  ggrepel        0.9.1   2021-01-15 [2] CRAN (R 4.1.1)
    #>  glue           1.4.2   2020-08-27 [2] CRAN (R 4.1.1)
    #>  gtable         0.3.0   2019-03-25 [2] CRAN (R 4.1.1)
    #>  hms            1.1.1   2021-09-26 [2] CRAN (R 4.1.1)
    #>  htmltools      0.5.2   2021-08-25 [2] CRAN (R 4.1.1)
    #>  httr           1.4.2   2020-07-20 [2] CRAN (R 4.1.1)
    #>  ISAnalytics  * 1.4.1   2021-10-28 [1] Bioconductor
    #>  jquerylib      0.1.4   2021-04-26 [2] CRAN (R 4.1.1)
    #>  jsonlite       1.7.2   2020-12-09 [2] CRAN (R 4.1.1)
    #>  knitr          1.36    2021-09-29 [2] CRAN (R 4.1.1)
    #>  lattice        0.20-45 2021-09-22 [2] CRAN (R 4.1.1)
    #>  lifecycle      1.0.1   2021-09-24 [2] CRAN (R 4.1.1)
    #>  lubridate      1.8.0   2021-10-07 [2] CRAN (R 4.1.1)
    #>  magrittr     * 2.0.1   2020-11-17 [2] CRAN (R 4.1.1)
    #>  mnormt         2.0.2   2020-09-01 [2] CRAN (R 4.1.1)
    #>  munsell        0.5.0   2018-06-12 [2] CRAN (R 4.1.1)
    #>  nlme           3.1-153 2021-09-07 [2] CRAN (R 4.1.1)
    #>  pillar         1.6.4   2021-10-18 [2] CRAN (R 4.1.1)
    #>  pkgconfig      2.0.3   2019-09-22 [2] CRAN (R 4.1.1)
    #>  plyr           1.8.6   2020-03-03 [2] CRAN (R 4.1.1)
    #>  psych          2.1.9   2021-09-22 [2] CRAN (R 4.1.1)
    #>  purrr          0.3.4   2020-04-17 [2] CRAN (R 4.1.1)
    #>  R6             2.5.1   2021-08-19 [2] CRAN (R 4.1.1)
    #>  Rcapture       1.4-3   2019-12-16 [2] CRAN (R 4.1.1)
    #>  Rcpp           1.0.7   2021-07-07 [2] CRAN (R 4.1.1)
    #>  readr          2.0.2   2021-09-27 [2] CRAN (R 4.1.1)
    #>  RefManageR   * 1.3.0   2020-11-13 [2] CRAN (R 4.1.1)
    #>  rlang          0.4.12  2021-10-18 [2] CRAN (R 4.1.1)
    #>  rmarkdown      2.11    2021-09-14 [2] CRAN (R 4.1.1)
    #>  sass           0.4.0   2021-05-12 [2] CRAN (R 4.1.1)
    #>  scales         1.1.1   2020-05-11 [2] CRAN (R 4.1.1)
    #>  sessioninfo  * 1.1.1   2018-11-05 [2] CRAN (R 4.1.1)
    #>  stringi        1.7.5   2021-10-04 [2] CRAN (R 4.1.1)
    #>  stringr        1.4.0   2019-02-10 [2] CRAN (R 4.1.1)
    #>  tibble         3.1.5   2021-09-30 [2] CRAN (R 4.1.1)
    #>  tidyr          1.1.4   2021-09-27 [2] CRAN (R 4.1.1)
    #>  tidyselect     1.1.1   2021-04-30 [2] CRAN (R 4.1.1)
    #>  tmvnsim        1.0-2   2016-12-15 [2] CRAN (R 4.1.1)
    #>  tzdb           0.2.0   2021-10-27 [2] CRAN (R 4.1.1)
    #>  utf8           1.2.2   2021-07-24 [2] CRAN (R 4.1.1)
    #>  vctrs          0.3.8   2021-04-29 [2] CRAN (R 4.1.1)
    #>  withr          2.4.2   2021-04-18 [2] CRAN (R 4.1.1)
    #>  xfun           0.27    2021-10-18 [2] CRAN (R 4.1.1)
    #>  xml2           1.3.2   2020-04-23 [2] CRAN (R 4.1.1)
    #>  yaml           2.2.1   2020-02-01 [2] CRAN (R 4.1.1)
    #>  zip            2.2.0   2021-05-31 [2] CRAN (R 4.1.1)
    #>
    #> [1] /tmp/RtmpAubEVU/Rinst20b77e2c74a653
    #> [2] /home/biocbuild/bbs-3.14-bioc/R/library

# 6 Bibliography

This vignette was generated using BiocStyle (Oleś, 2021) with knitr (Xie, 2021) and rmarkdown (Allaire, Xie, McPherson, Luraschi, Ushey, Atkins, Wickham, Cheng, Chang, and Iannone, 2021) running behind the scenes.

Citations made with RefManageR (McLean, 2017).

[1] J. Allaire, Y. Xie, J. McPherson, et al. rmarkdown: Dynamic Documents for R. R package version 2.11. 2021. URL: https://github.com/rstudio/rmarkdown.

[2] M. W. McLean. “RefManageR: Import and Manage BibTeX and BibLaTeX References in R”. In: The Journal of Open Source Software (2017). DOI: 10.21105/joss.00338.

[3] A. Oleś. BiocStyle: Standard styles for vignettes and other Bioconductor documents. R package version 2.22.0. 2021. URL: https://github.com/Bioconductor/BiocStyle.

[4] Y. Xie. knitr: A General-Purpose Package for Dynamic Report Generation in R. R package version 1.36. 2021. URL: https://yihui.org/knitr/.