Authors: Koki Tsuyuzaki [aut, cre], Manabu Ishii [aut], Itoshi Nikaido [aut]
Last modified: 2023-03-28 14:08:49.234662
Compiled: Tue Mar 28 14:10:44 2023

1 Installation

To install this package, start R (>= 4.1.0) and enter:

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

2 Fetch LRBaseDb databases from AnnotationHub

The AHLRBaseDbs package provides the metadata for all LRBaseDb SQLite databases in AnnotationHub. First we load/update the AnnotationHub resource.

library(AnnotationHub)
ah <- AnnotationHub()

Next we list all LRBaseDb entries from AnnotationHub.

query(ah, "LRBaseDb")
## AnnotationHub with 625 records
## # snapshotDate(): 2023-03-28
## # $dataprovider: FANTOM5,DLRP,IUPHAR,HPRD,STRING,SWISSPROT,TREMBL,ENSEMBL,CE...
## # $species: Xenopus tropicalis, Vulpes vulpes, Ursus maritimus, Takifugu rub...
## # $rdataclass: SQLiteFile
## # additional mcols(): taxonomyid, genome, description,
## #   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
## #   rdatapath, sourceurl, sourcetype 
## # retrieve records with, e.g., 'object[["AH91646"]]' 
## 
##              title                                                         
##   AH91646  | LRBaseDb for Anolis carolinensis (Anole lizard, v001)         
##   AH91647  | LRBaseDb for Aquila chrysaetos chrysaetos (Golden eagle, v001)
##   AH91648  | LRBaseDb for Astatotilapia calliptera (Eastern happy, v001)   
##   AH91649  | LRBaseDb for Anopheles gambiae str. PEST (Anopheline, v001)   
##   AH91650  | LRBaseDb for Ailuropoda melanoleuca (Panda, v001)             
##   ...        ...                                                           
##   AH111454 | LRBaseDb for Taeniopygia guttata (Zebra finch, v005)          
##   AH111455 | LRBaseDb for Takifugu rubripes (Fugu, v005)                   
##   AH111456 | LRBaseDb for Ursus maritimus (Polar bear, v005)               
##   AH111457 | LRBaseDb for Vulpes vulpes (Red fox, v005)                    
##   AH111458 | LRBaseDb for Xenopus tropicalis (Tropical clawed frog, v005)

We can confirm the metadata in AnnotationHub in Bioconductor S3 bucket with mcols().

mcols(query(ah, "LRBaseDb"))
## DataFrame with 625 rows and 15 columns
##                           title           dataprovider                species
##                     <character>            <character>            <character>
## AH91646  LRBaseDb for Anolis .. FANTOM5,DLRP,IUPHAR,..    Anolis carolinensis
## AH91647  LRBaseDb for Aquila .. FANTOM5,DLRP,IUPHAR,.. Aquila chrysaetos ch..
## AH91648  LRBaseDb for Astatot.. FANTOM5,DLRP,IUPHAR,.. Astatotilapia callip..
## AH91649  LRBaseDb for Anophel.. FANTOM5,DLRP,IUPHAR,.. Anopheles gambiae st..
## AH91650  LRBaseDb for Ailurop.. FANTOM5,DLRP,IUPHAR,.. Ailuropoda melanoleuca
## ...                         ...                    ...                    ...
## AH111454 LRBaseDb for Taeniop.. FANTOM5,DLRP,IUPHAR,..    Taeniopygia guttata
## AH111455 LRBaseDb for Takifug.. FANTOM5,DLRP,IUPHAR,..      Takifugu rubripes
## AH111456 LRBaseDb for Ursus m.. FANTOM5,DLRP,IUPHAR,..        Ursus maritimus
## AH111457 LRBaseDb for Vulpes .. FANTOM5,DLRP,IUPHAR,..          Vulpes vulpes
## AH111458 LRBaseDb for Xenopus.. FANTOM5,DLRP,IUPHAR,..     Xenopus tropicalis
##          taxonomyid      genome            description coordinate_1_based
##           <integer> <character>            <character>          <integer>
## AH91646       28377          NA Correspondence table..                  1
## AH91647      223781          NA Correspondence table..                  1
## AH91648        8154          NA Correspondence table..                  1
## AH91649      180454          NA Correspondence table..                  1
## AH91650        9646          NA Correspondence table..                  1
## ...             ...         ...                    ...                ...
## AH111454      59729          NA Correspondence table..                  1
## AH111455      31033          NA Correspondence table..                  1
## AH111456      29073          NA Correspondence table..                  1
## AH111457       9627          NA Correspondence table..                  1
## AH111458       8364          NA Correspondence table..                  1
##                      maintainer rdatadateadded preparerclass
##                     <character>    <character>   <character>
## AH91646  Koki Tsuyuzaki <k.t...     2021-04-19   AHLRBaseDbs
## AH91647  Koki Tsuyuzaki <k.t...     2021-04-19   AHLRBaseDbs
## AH91648  Koki Tsuyuzaki <k.t...     2021-04-19   AHLRBaseDbs
## AH91649  Koki Tsuyuzaki <k.t...     2021-04-19   AHLRBaseDbs
## AH91650  Koki Tsuyuzaki <k.t...     2021-04-19   AHLRBaseDbs
## ...                         ...            ...           ...
## AH111454 Koki Tsuyuzaki <k.t...     2023-03-28   AHLRBaseDbs
## AH111455 Koki Tsuyuzaki <k.t...     2023-03-28   AHLRBaseDbs
## AH111456 Koki Tsuyuzaki <k.t...     2023-03-28   AHLRBaseDbs
## AH111457 Koki Tsuyuzaki <k.t...     2023-03-28   AHLRBaseDbs
## AH111458 Koki Tsuyuzaki <k.t...     2023-03-28   AHLRBaseDbs
##                                                      tags  rdataclass
##                                                    <AsIs> <character>
## AH91646   Annotation,Anole lizard,Anolis carolinensis,...  SQLiteFile
## AH91647    Annotation,Aquila chrysaetos ch..,BADERLAB,...  SQLiteFile
## AH91648    Annotation,Astatotilapia callip..,BADERLAB,...  SQLiteFile
## AH91649  Annotation,Anopheles gambiae st..,Anopheline,...  SQLiteFile
## AH91650    Ailuropoda melanoleuca,Annotation,BADERLAB,...  SQLiteFile
## ...                                                   ...         ...
## AH111454                  Annotation,BADERLAB,BIOMART,...  SQLiteFile
## AH111455                  Annotation,BADERLAB,BIOMART,...  SQLiteFile
## AH111456                  Annotation,BADERLAB,BIOMART,...  SQLiteFile
## AH111457                  Annotation,BADERLAB,BIOMART,...  SQLiteFile
## AH111458                  Annotation,BADERLAB,BIOMART,...  SQLiteFile
##                       rdatapath              sourceurl  sourcetype
##                     <character>            <character> <character>
## AH91646  AHLRBaseDbs/v001/LRB.. https://github.com/r..         CSV
## AH91647  AHLRBaseDbs/v001/LRB.. https://github.com/r..         CSV
## AH91648  AHLRBaseDbs/v001/LRB.. https://github.com/r..         CSV
## AH91649  AHLRBaseDbs/v001/LRB.. https://github.com/r..         CSV
## AH91650  AHLRBaseDbs/v001/LRB.. https://github.com/r..         CSV
## ...                         ...                    ...         ...
## AH111454 AHLRBaseDbs/v005/LRB.. https://github.com/r..         CSV
## AH111455 AHLRBaseDbs/v005/LRB.. https://github.com/r..         CSV
## AH111456 AHLRBaseDbs/v005/LRB.. https://github.com/r..         CSV
## AH111457 AHLRBaseDbs/v005/LRB.. https://github.com/r..         CSV
## AH111458 AHLRBaseDbs/v005/LRB.. https://github.com/r..         CSV

We can query only the LRBaseDb SQLite files for species Mus musculus.

qr <- query(ah, c("LRBaseDb", "Mus musculus"))
# filepath_mmu <- qr[[1]]

This filepath is can be specified with the argument of RSQLite::dbConnect and LRBaseDbi::LRBaseDb and also used as the argument of scTensor, which is an R/Bioconductor package for the detection of cell-cell interaction detection.

For the details, check the vignettes of RSQLite, LRBaseDbi, and scTensor.

Session information

## R Under development (unstable) (2023-01-05 r83566)
## Platform: x86_64-apple-darwin21.6.0 (64-bit)
## Running under: macOS Monterey 12.6.2
## 
## Matrix products: default
## BLAS:   /Users/ka36530/R-stuff/bin/R-devel/lib/libRblas.dylib 
## LAPACK: /Users/ka36530/R-stuff/bin/R-devel/lib/libRlapack.dylib;  LAPACK version 3.11.0
## 
## locale:
## [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## time zone: America/New_York
## tzcode source: system (macOS)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] AnnotationHub_3.7.1 BiocFileCache_2.7.1 dbplyr_2.3.0       
## [4] BiocGenerics_0.45.0 BiocStyle_2.27.1   
## 
## loaded via a namespace (and not attached):
##  [1] KEGGREST_1.39.0               xfun_0.37                    
##  [3] bslib_0.4.2                   Biobase_2.59.0               
##  [5] bitops_1.0-7                  vctrs_0.5.2                  
##  [7] tools_4.3.0                   generics_0.1.3               
##  [9] stats4_4.3.0                  curl_5.0.0                   
## [11] tibble_3.1.8                  fansi_1.0.4                  
## [13] AnnotationDbi_1.61.0          RSQLite_2.2.20               
## [15] blob_1.2.3                    pkgconfig_2.0.3              
## [17] S4Vectors_0.37.3              assertthat_0.2.1             
## [19] GenomeInfoDbData_1.2.9        lifecycle_1.0.3              
## [21] compiler_4.3.0                Biostrings_2.67.0            
## [23] GenomeInfoDb_1.35.15          httpuv_1.6.9                 
## [25] htmltools_0.5.4               sass_0.4.5                   
## [27] RCurl_1.98-1.10               yaml_2.3.7                   
## [29] interactiveDisplayBase_1.37.0 pillar_1.8.1                 
## [31] later_1.3.0                   crayon_1.5.2                 
## [33] jquerylib_0.1.4               ellipsis_0.3.2               
## [35] cachem_1.0.6                  mime_0.12                    
## [37] tidyselect_1.2.0              digest_0.6.31                
## [39] purrr_1.0.1                   dplyr_1.1.0                  
## [41] bookdown_0.32                 BiocVersion_3.17.1           
## [43] fastmap_1.1.0                 cli_3.6.0                    
## [45] magrittr_2.0.3                utf8_1.2.3                   
## [47] withr_2.5.0                   filelock_1.0.2               
## [49] promises_1.2.0.1              rappdirs_0.3.3               
## [51] bit64_4.0.5                   rmarkdown_2.20               
## [53] XVector_0.39.0                httr_1.4.4                   
## [55] bit_4.0.5                     png_0.1-8                    
## [57] memoise_2.0.1                 shiny_1.7.4                  
## [59] evaluate_0.20                 knitr_1.42                   
## [61] IRanges_2.33.0                rlang_1.0.6                  
## [63] Rcpp_1.0.10                   xtable_1.8-4                 
## [65] glue_1.6.2                    DBI_1.1.3                    
## [67] BiocManager_1.30.19           jsonlite_1.8.4               
## [69] R6_2.5.1                      zlibbioc_1.45.0