Annotate features in a Seurat object with additional metadata from databases or a GTF file.
Usage
AnnotateFeatures(
srt,
species = "Homo_sapiens",
IDtype = c("symbol", "ensembl_id", "entrez_id"),
db = NULL,
db_update = FALSE,
db_version = "latest",
convert_species = TRUE,
Ensembl_version = 103,
mirror = NULL,
gtf = NULL,
merge_gtf_by = "gene_name",
columns = c("seqname", "feature", "start", "end", "strand", "gene_id", "gene_name",
"gene_type"),
assays = "RNA",
overwrite = FALSE
)Arguments
- srt
Seurat object to be annotated.
- species
Name of the species to be used for annotation. Default is "Homo_sapiens".
- IDtype
Type of identifier to use for annotation. Default is "symbol" with options "symbol", "ensembl_id", and "entrez_id".
- db
Vector of database names to be used for annotation. Default is NULL.
- db_update
Logical value indicating whether to update the database. Default is FALSE.
- db_version
Version of the database to use. Default is "latest".
- convert_species
Whether to use a species-converted database when the annotation is missing for the specified species. The default value is TRUE.
- Ensembl_version
Version of the Ensembl database to use. Default is 103.
- mirror
URL of the mirror to use for Ensembl database. Default is NULL.
- gtf
Path to the GTF file to be used for annotation. Default is NULL.
- merge_gtf_by
Column name to merge the GTF file by. Default is "gene_name".
- columns
Vector of column names to be used from the GTF file. Default is "seqname", "feature", "start", "end", "strand", "gene_id", "gene_name", "gene_type".
- assays
Character vector of assay names to be annotated. Default is "RNA".
- overwrite
Logical value indicating whether to overwrite existing metadata. Default is FALSE.
Examples
data(pancreas_sub)
pancreas_sub <- AnnotateFeatures(
pancreas_sub,
species = "Mus_musculus",
db = c(
"Chromosome",
"GeneType",
"Enzyme",
"TF",
"CSPA",
"VerSeDa"
)
)
#> ℹ [2025-09-20 12:52:28] Species: Mus_musculus
#> ℹ [2025-09-20 12:52:28] Installing: org.Mm.eg.db...
#> ℹ Loading metadata database
#> ✔ Loading metadata database ... done
#>
#>
#> → Will install 37 packages.
#> → All 37 packages (0 B) are cached.
#> + AnnotationDbi 1.70.0 [bld]
#> + Biobase 2.68.0 [bld][cmp]
#> + BiocGenerics 0.54.0 [bld]
#> + Biostrings 2.76.0 [bld][cmp]
#> + DBI 1.2.3
#> + GenomeInfoDb 1.44.2 [bld]
#> + GenomeInfoDbData 1.2.14 [bld]
#> + IRanges 2.42.0 [bld][cmp]
#> + KEGGREST 1.48.1 [bld]
#> + R6 2.6.1
#> + RSQLite 2.4.3
#> + S4Vectors 0.46.0 [bld][cmp]
#> + UCSC.utils 1.4.0 [bld]
#> + XVector 0.48.0 [bld][cmp]
#> + askpass 1.2.1
#> + bit 4.6.0
#> + bit64 4.6.0-1
#> + blob 1.2.4
#> + cachem 1.1.0
#> + cli 3.6.5
#> + crayon 1.5.3
#> + curl 7.0.0 + ✔ libcurl4-openssl-dev, ✔ libssl-dev
#> + fastmap 1.2.0
#> + generics 0.1.4
#> + glue 1.8.0
#> + httr 1.4.7
#> + jsonlite 2.0.0
#> + lifecycle 1.0.4
#> + memoise 2.0.1
#> + mime 0.13
#> + openssl 2.3.3 + ✔ libssl-dev
#> + org.Mm.eg.db 3.21.0 [bld]
#> + pkgconfig 2.0.3
#> + png 0.1-8 + ✔ libpng-dev
#> + rlang 1.1.6
#> + sys 3.4.3
#> + vctrs 0.6.5
#> ✔ All system requirements are already installed.
#>
#> ℹ No downloads are needed, 37 pkgs are cached
#> ✔ Got blob 1.2.4 (x86_64-pc-linux-gnu-ubuntu-24.04) (47.47 kB)
#> ✔ Got BiocGenerics 0.54.0 (source) (56.09 kB)
#> ✔ Got askpass 1.2.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (21.89 kB)
#> ✔ Got cachem 1.1.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (67.49 kB)
#> ✔ Got fastmap 1.2.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (66.05 kB)
#> ✔ Got KEGGREST 1.48.1 (source) (239.15 kB)
#> ✔ Got IRanges 2.42.0 (source) (483.03 kB)
#> ✔ Got bit64 4.6.0-1 (x86_64-pc-linux-gnu-ubuntu-24.04) (492.54 kB)
#> ✔ Got httr 1.4.7 (x86_64-pc-linux-gnu-ubuntu-24.04) (486.52 kB)
#> ✔ Got pkgconfig 2.0.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (18.08 kB)
#> ✔ Got bit 4.6.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (628.10 kB)
#> ✔ Got lifecycle 1.0.4 (x86_64-pc-linux-gnu-ubuntu-24.04) (125.07 kB)
#> ✔ Got png 0.1-8 (x86_64-pc-linux-gnu-ubuntu-24.04) (40.57 kB)
#> ✔ Got glue 1.8.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (168.12 kB)
#> ✔ Got R6 2.6.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (86.81 kB)
#> ✔ Got crayon 1.5.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (163.30 kB)
#> ✔ Got memoise 2.0.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (48.86 kB)
#> ✔ Got mime 0.13 (x86_64-pc-linux-gnu-ubuntu-24.04) (44.52 kB)
#> ✔ Got sys 3.4.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (40.73 kB)
#> ✔ Got cli 3.6.5 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.34 MB)
#> ✔ Got vctrs 0.6.5 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.31 MB)
#> ✔ Got DBI 1.2.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (916.93 kB)
#> ✔ Got rlang 1.1.6 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.59 MB)
#> ✔ Got S4Vectors 0.46.0 (source) (1.07 MB)
#> ✔ Got generics 0.1.4 (x86_64-pc-linux-gnu-ubuntu-24.04) (80.38 kB)
#> ✔ Got curl 7.0.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (788.30 kB)
#> ✔ Got XVector 0.48.0 (source) (67.89 kB)
#> ✔ Got Biobase 2.68.0 (source) (1.98 MB)
#> ✔ Got UCSC.utils 1.4.0 (source) (236.15 kB)
#> ✔ Got openssl 2.3.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.31 MB)
#> ✔ Got RSQLite 2.4.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.35 MB)
#> ✔ Got jsonlite 2.0.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.09 MB)
#> ✔ Got GenomeInfoDb 1.44.2 (source) (3.59 MB)
#> ✔ Got AnnotationDbi 1.70.0 (source) (4.37 MB)
#> ✔ Got Biostrings 2.76.0 (source) (12.82 MB)
#> ✔ Got GenomeInfoDbData 1.2.14 (source) (13.24 MB)
#> ✔ Got org.Mm.eg.db 3.21.0 (source) (86.57 MB)
#> ℹ Installing system requirements
#> ℹ Executing `sudo sh -c apt-get -y update`
#> Get:1 file:/etc/apt/apt-mirrors.txt Mirrorlist [144 B]
#> Hit:6 https://packages.microsoft.com/repos/azure-cli noble InRelease
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#> Hit:5 http://azure.archive.ubuntu.com/ubuntu noble-security InRelease
#> Reading package lists...
#> ℹ Executing `sudo sh -c apt-get -y install libcurl4-openssl-dev libssl-dev libpng-dev`
#> Reading package lists...
#> Building dependency tree...
#> Reading state information...
#> libcurl4-openssl-dev is already the newest version (8.5.0-2ubuntu10.6).
#> libssl-dev is already the newest version (3.0.13-0ubuntu3.5).
#> libpng-dev is already the newest version (1.6.43-5build1).
#> 0 upgraded, 0 newly installed, 0 to remove and 41 not upgraded.
#> ℹ Building GenomeInfoDbData 1.2.14
#> ✔ Installed askpass 1.2.1 (87ms)
#> ✔ Installed bit 4.6.0 (95ms)
#> ✔ Installed bit64 4.6.0-1 (120ms)
#> ✔ Installed blob 1.2.4 (62ms)
#> ✔ Installed cachem 1.1.0 (106ms)
#> ✔ Installed cli 3.6.5 (107ms)
#> ✔ Installed crayon 1.5.3 (65ms)
#> ✔ Installed curl 7.0.0 (68ms)
#> ✔ Installed DBI 1.2.3 (66ms)
#> ✔ Installed fastmap 1.2.0 (62ms)
#> ✔ Installed generics 0.1.4 (83ms)
#> ℹ Building BiocGenerics 0.54.0
#> ✔ Installed glue 1.8.0 (99ms)
#> ✔ Installed httr 1.4.7 (46ms)
#> ✔ Installed lifecycle 1.0.4 (41ms)
#> ✔ Installed jsonlite 2.0.0 (139ms)
#> ✔ Installed memoise 2.0.1 (95ms)
#> ✔ Installed mime 0.13 (98ms)
#> ✔ Installed openssl 2.3.3 (116ms)
#> ✔ Installed pkgconfig 2.0.3 (92ms)
#> ✔ Installed png 0.1-8 (85ms)
#> ✔ Built GenomeInfoDbData 1.2.14 (1.8s)
#> ✔ Installed R6 2.6.1 (452ms)
#> ✔ Installed rlang 1.1.6 (109ms)
#> ✔ Installed RSQLite 2.4.3 (71ms)
#> ✔ Installed sys 3.4.3 (67ms)
#> ✔ Installed vctrs 0.6.5 (68ms)
#> ✔ Installed GenomeInfoDbData 1.2.14 (90ms)
#> ✔ Built BiocGenerics 0.54.0 (3s)
#> ✔ Installed BiocGenerics 0.54.0 (1s)
#> ℹ Building Biobase 2.68.0
#> ℹ Building S4Vectors 0.46.0
#> ✔ Built Biobase 2.68.0 (6.6s)
#> ✔ Installed Biobase 2.68.0 (1.1s)
#> ✔ Built S4Vectors 0.46.0 (15.7s)
#> ✔ Installed S4Vectors 0.46.0 (1s)
#> ℹ Building IRanges 2.42.0
#> ℹ Building UCSC.utils 1.4.0
#> ✔ Built UCSC.utils 1.4.0 (2.4s)
#> ✔ Installed UCSC.utils 1.4.0 (1s)
#> ✔ Built IRanges 2.42.0 (35.2s)
#> ✔ Installed IRanges 2.42.0 (1s)
#> ℹ Building GenomeInfoDb 1.44.2
#> ℹ Building XVector 0.48.0
#> ✔ Built GenomeInfoDb 1.44.2 (7.1s)
#> ✔ Installed GenomeInfoDb 1.44.2 (100ms)
#> ✔ Built XVector 0.48.0 (8.7s)
#> ✔ Installed XVector 0.48.0 (1s)
#> ℹ Building Biostrings 2.76.0
#> ✔ Built Biostrings 2.76.0 (18.4s)
#> ✔ Installed Biostrings 2.76.0 (1.1s)
#> ℹ Building KEGGREST 1.48.1
#> ✔ Built KEGGREST 1.48.1 (4.5s)
#> ✔ Installed KEGGREST 1.48.1 (1s)
#> ℹ Building AnnotationDbi 1.70.0
#> ✔ Built AnnotationDbi 1.70.0 (11.4s)
#> ✔ Installed AnnotationDbi 1.70.0 (1.1s)
#> ℹ Building org.Mm.eg.db 3.21.0
#> ✔ Built org.Mm.eg.db 3.21.0 (3m 7.4s)
#> ✔ Installed org.Mm.eg.db 3.21.0 (3s)
#> ✔ 1 pkg + 36 deps: added 37, dld 37 (137.04 MB) [5m 22.3s]
#> ℹ [2025-09-20 12:57:51] Installing: GO.db...
#>
#> → Will install 1 package.
#> → The package (0 B) is cached.
#> + GO.db 3.21.0 [bld]
#> ✔ All system requirements are already installed.
#>
#> ℹ No downloads are needed, 1 pkg is cached
#> ✔ Got GO.db 3.21.0 (source) (25.56 MB)
#> ℹ Installing system requirements
#> ℹ Executing `sudo sh -c apt-get -y update`
#> Get:1 file:/etc/apt/apt-mirrors.txt Mirrorlist [144 B]
#> Hit:2 http://azure.archive.ubuntu.com/ubuntu noble InRelease
#> Hit:3 http://azure.archive.ubuntu.com/ubuntu noble-updates InRelease
#> Hit:6 https://packages.microsoft.com/repos/azure-cli noble InRelease
#> Hit:4 http://azure.archive.ubuntu.com/ubuntu noble-backports InRelease
#> Hit:5 http://azure.archive.ubuntu.com/ubuntu noble-security InRelease
#> Hit:7 https://packages.microsoft.com/ubuntu/24.04/prod noble InRelease
#> Reading package lists...
#> ℹ Executing `sudo sh -c apt-get -y install libcurl4-openssl-dev libssl-dev libpng-dev`
#> Reading package lists...
#> Building dependency tree...
#> Reading state information...
#> libcurl4-openssl-dev is already the newest version (8.5.0-2ubuntu10.6).
#> libssl-dev is already the newest version (3.0.13-0ubuntu3.5).
#> libpng-dev is already the newest version (1.6.43-5build1).
#> 0 upgraded, 0 newly installed, 0 to remove and 41 not upgraded.
#> ℹ Building GO.db 3.21.0
#> ✔ Built GO.db 3.21.0 (37.1s)
#> ✔ Installed GO.db 3.21.0 (448ms)
#> ✔ 1 pkg + 36 deps: kept 36, added 1, dld 1 (25.56 MB) [43.5s]
#> ℹ [2025-09-20 12:58:34] Installing: GOSemSim...
#>
#> → Will install 9 packages.
#> → All 9 packages (0 B) are cached.
#> + GOSemSim 2.34.0 [bld][cmp]
#> + R.methodsS3 1.8.2
#> + R.oo 1.27.1
#> + R.utils 2.13.0
#> + Rcpp 1.1.0
#> + digest 0.6.37
#> + fs 1.6.6 + ✔ make
#> + rappdirs 0.3.3
#> + yulab.utils 0.2.1
#> ✔ All system requirements are already installed.
#>
#> ℹ No downloads are needed, 9 pkgs are cached
#> ✔ Got GOSemSim 2.34.0 (source) (608.98 kB)
#> ✔ Got rappdirs 0.3.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (45.26 kB)
#> ✔ Got R.methodsS3 1.8.2 (x86_64-pc-linux-gnu-ubuntu-24.04) (82.67 kB)
#> ✔ Got digest 0.6.37 (x86_64-pc-linux-gnu-ubuntu-24.04) (227.14 kB)
#> ✔ Got yulab.utils 0.2.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (119.17 kB)
#> ✔ Got fs 1.6.6 (x86_64-pc-linux-gnu-ubuntu-24.04) (310.07 kB)
#> ✔ Got R.oo 1.27.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (996.09 kB)
#> ✔ Got R.utils 2.13.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.45 MB)
#> ✔ Got Rcpp 1.1.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (2.19 MB)
#> ℹ Installing system requirements
#> ℹ Executing `sudo sh -c apt-get -y update`
#> Get:1 file:/etc/apt/apt-mirrors.txt Mirrorlist [144 B]
#> Hit:2 http://azure.archive.ubuntu.com/ubuntu noble InRelease
#> Hit:6 https://packages.microsoft.com/repos/azure-cli noble InRelease
#> Hit:7 https://packages.microsoft.com/ubuntu/24.04/prod noble InRelease
#> Hit:3 http://azure.archive.ubuntu.com/ubuntu noble-updates InRelease
#> Hit:4 http://azure.archive.ubuntu.com/ubuntu noble-backports InRelease
#> Hit:5 http://azure.archive.ubuntu.com/ubuntu noble-security InRelease
#> Reading package lists...
#> ℹ Executing `sudo sh -c apt-get -y install make libcurl4-openssl-dev libssl-dev libpng-dev`
#> Reading package lists...
#> Building dependency tree...
#> Reading state information...
#> make is already the newest version (4.3-4.1build2).
#> libcurl4-openssl-dev is already the newest version (8.5.0-2ubuntu10.6).
#> libssl-dev is already the newest version (3.0.13-0ubuntu3.5).
#> libpng-dev is already the newest version (1.6.43-5build1).
#> 0 upgraded, 0 newly installed, 0 to remove and 41 not upgraded.
#> ✔ Installed digest 0.6.37 (60ms)
#> ✔ Installed fs 1.6.6 (77ms)
#> ✔ Installed R.methodsS3 1.8.2 (128ms)
#> ✔ Installed R.oo 1.27.1 (156ms)
#> ✔ Installed R.utils 2.13.0 (58ms)
#> ✔ Installed rappdirs 0.3.3 (59ms)
#> ✔ Installed Rcpp 1.1.0 (67ms)
#> ✔ Installed yulab.utils 0.2.1 (45ms)
#> ℹ Building GOSemSim 2.34.0
#> ✔ Built GOSemSim 2.34.0 (13.5s)
#> ✔ Installed GOSemSim 2.34.0 (37ms)
#> ✔ 1 pkg + 45 deps: kept 37, added 9, dld 9 (6.03 MB) [17.9s]
#> ℹ [2025-09-20 12:58:52] org.Mm.eg.db, GO.db, and GOSemSim installed successfully
#> ℹ [2025-09-20 12:58:53] Preparing database: Chromosome
#> ℹ [2025-09-20 12:58:53] Preparing database: GeneType
#> ℹ [2025-09-20 12:58:54] Preparing database: Enzyme
#> ℹ [2025-09-20 12:58:56] Preparing database: TF
#> ℹ [2025-09-20 12:58:58] Error in utils::download.file(url = url, destfile = destfile, method = method, : cannot open URL 'https://guolab.wchscu.cn/AnimalTFDB4_static/download/TF_list_final/Mus_musculus_TF'
#> ! [2025-09-20 12:58:58] Failed to download using auto, from <https://guolab.wchscu.cn/AnimalTFDB4_static/download/TF_list_final/Mus_musculus_TF>
#> ℹ [2025-09-20 12:59:00] Error in utils::download.file(url = url, destfile = destfile, method = method, : 'wget' call had nonzero exit status
#> ! [2025-09-20 12:59:00] Failed to download using wget, from <https://guolab.wchscu.cn/AnimalTFDB4_static/download/TF_list_final/Mus_musculus_TF>
#> ℹ [2025-09-20 12:59:02] Error in utils::download.file(url = url, destfile = destfile, method = method, : cannot open URL 'https://guolab.wchscu.cn/AnimalTFDB4_static/download/TF_list_final/Mus_musculus_TF'
#> ! [2025-09-20 12:59:02] Failed to download using libcurl, from <https://guolab.wchscu.cn/AnimalTFDB4_static/download/TF_list_final/Mus_musculus_TF>
#> Warning: incomplete final line found by readTableHeader on '/tmp/Rtmp8qFX1m/file266a43d4373b'
#> ℹ [2025-09-20 12:59:05] Error in utils::download.file(url = url, destfile = destfile, method = method, : cannot open URL 'https://guolab.wchscu.cn/AnimalTFDB4_static/download/Cof_list_final/Mus_musculus_Cof'
#> ! [2025-09-20 12:59:05] Failed to download using auto, from <https://guolab.wchscu.cn/AnimalTFDB4_static/download/Cof_list_final/Mus_musculus_Cof>
#> ℹ [2025-09-20 12:59:08] Error in utils::download.file(url = url, destfile = destfile, method = method, : 'wget' call had nonzero exit status
#> ! [2025-09-20 12:59:08] Failed to download using wget, from <https://guolab.wchscu.cn/AnimalTFDB4_static/download/Cof_list_final/Mus_musculus_Cof>
#> ℹ [2025-09-20 12:59:10] Error in utils::download.file(url = url, destfile = destfile, method = method, : cannot open URL 'https://guolab.wchscu.cn/AnimalTFDB4_static/download/Cof_list_final/Mus_musculus_Cof'
#> ! [2025-09-20 12:59:10] Failed to download using libcurl, from <https://guolab.wchscu.cn/AnimalTFDB4_static/download/Cof_list_final/Mus_musculus_Cof>
#> Warning: incomplete final line found by readTableHeader on '/tmp/Rtmp8qFX1m/file266a43d4373b'
#> ! [2025-09-20 12:59:12] Use the human annotation to create the TF database for Mus_musculus
#> ℹ [2025-09-20 12:59:13] Error in utils::download.file(url = url, destfile = destfile, method = method, : cannot open URL 'https://guolab.wchscu.cn/AnimalTFDB4_static/download/TF_list_final/Homo_sapiens_TF'
#> ! [2025-09-20 12:59:13] Failed to download using auto, from <https://guolab.wchscu.cn/AnimalTFDB4_static/download/TF_list_final/Homo_sapiens_TF>
#> ℹ [2025-09-20 12:59:15] Error in utils::download.file(url = url, destfile = destfile, method = method, : 'wget' call had nonzero exit status
#> ! [2025-09-20 12:59:15] Failed to download using wget, from <https://guolab.wchscu.cn/AnimalTFDB4_static/download/TF_list_final/Homo_sapiens_TF>
#> ℹ [2025-09-20 12:59:18] Error in utils::download.file(url = url, destfile = destfile, method = method, : cannot open URL 'https://guolab.wchscu.cn/AnimalTFDB4_static/download/TF_list_final/Homo_sapiens_TF'
#> ! [2025-09-20 12:59:18] Failed to download using libcurl, from <https://guolab.wchscu.cn/AnimalTFDB4_static/download/TF_list_final/Homo_sapiens_TF>
#> Warning: incomplete final line found by readTableHeader on '/tmp/Rtmp8qFX1m/file266a43d4373b'
#> ℹ [2025-09-20 12:59:21] Error in utils::download.file(url = url, destfile = destfile, method = method, : cannot open URL 'https://guolab.wchscu.cn/AnimalTFDB4_static/download/Cof_list_final/Homo_sapiens_Cof'
#> ! [2025-09-20 12:59:21] Failed to download using auto, from <https://guolab.wchscu.cn/AnimalTFDB4_static/download/Cof_list_final/Homo_sapiens_Cof>
#> ℹ [2025-09-20 12:59:23] Error in utils::download.file(url = url, destfile = destfile, method = method, : 'wget' call had nonzero exit status
#> ! [2025-09-20 12:59:23] Failed to download using wget, from <https://guolab.wchscu.cn/AnimalTFDB4_static/download/Cof_list_final/Homo_sapiens_Cof>
#> ℹ [2025-09-20 12:59:25] Error in utils::download.file(url = url, destfile = destfile, method = method, : cannot open URL 'https://guolab.wchscu.cn/AnimalTFDB4_static/download/Cof_list_final/Homo_sapiens_Cof'
#> ! [2025-09-20 12:59:25] Failed to download using libcurl, from <https://guolab.wchscu.cn/AnimalTFDB4_static/download/Cof_list_final/Homo_sapiens_Cof>
#> Warning: incomplete final line found by readTableHeader on '/tmp/Rtmp8qFX1m/file266a43d4373b'
#> Error in data.frame(Term = "TF", symbol = tf[["Symbol"]]): arguments imply differing number of rows: 1, 0
head(
GetFeaturesData(
pancreas_sub,
assays = "RNA"
)
)
#> data frame with 0 columns and 6 rows
if (FALSE) { # \dontrun{
# Annotate features using a GTF file
pancreas_sub <- AnnotateFeatures(
pancreas_sub,
gtf = "/refdata-gex-mm10-2020-A/genes/genes.gtf"
)
head(
GetFeaturesData(
pancreas_sub,
assays = "RNA"
)
)
} # }