Authors: Koki Tsuyuzaki [aut, cre], Manabu Ishii [aut], Itoshi Nikaido [aut]
Last modified: 2023-10-17 09:41:25.611888
Compiled: Tue Oct 17 09:44:31 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 749 records
## # snapshotDate(): 2023-10-05
## # $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)             
##   ...        ...                                                           
##   AH113975 | LRBaseDb for Taeniopygia guttata (Zebra finch, v006)          
##   AH113976 | LRBaseDb for Takifugu rubripes (Fugu, v006)                   
##   AH113977 | LRBaseDb for Ursus maritimus (Polar bear, v006)               
##   AH113978 | LRBaseDb for Vulpes vulpes (Red fox, v006)                    
##   AH113979 | LRBaseDb for Xenopus tropicalis (Tropical clawed frog, v006)

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

mcols(query(ah, "LRBaseDb"))
## DataFrame with 749 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
## ...                         ...                    ...                    ...
## AH113975 LRBaseDb for Taeniop.. FANTOM5,DLRP,IUPHAR,..    Taeniopygia guttata
## AH113976 LRBaseDb for Takifug.. FANTOM5,DLRP,IUPHAR,..      Takifugu rubripes
## AH113977 LRBaseDb for Ursus m.. FANTOM5,DLRP,IUPHAR,..        Ursus maritimus
## AH113978 LRBaseDb for Vulpes .. FANTOM5,DLRP,IUPHAR,..          Vulpes vulpes
## AH113979 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
## ...             ...         ...                    ...                ...
## AH113975      59729          NA Correspondence table..                  1
## AH113976      31033          NA Correspondence table..                  1
## AH113977      29073          NA Correspondence table..                  1
## AH113978       9627          NA Correspondence table..                  1
## AH113979       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
## ...                         ...            ...           ...
## AH113975 Koki Tsuyuzaki <k.t...     2023-09-27   AHLRBaseDbs
## AH113976 Koki Tsuyuzaki <k.t...     2023-09-27   AHLRBaseDbs
## AH113977 Koki Tsuyuzaki <k.t...     2023-09-27   AHLRBaseDbs
## AH113978 Koki Tsuyuzaki <k.t...     2023-09-27   AHLRBaseDbs
## AH113979 Koki Tsuyuzaki <k.t...     2023-09-27   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
## ...                                                   ...         ...
## AH113975                  Annotation,BADERLAB,BIOMART,...  SQLiteFile
## AH113976                  Annotation,BADERLAB,BIOMART,...  SQLiteFile
## AH113977                  Annotation,BADERLAB,BIOMART,...  SQLiteFile
## AH113978                  Annotation,BADERLAB,BIOMART,...  SQLiteFile
## AH113979                  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
## ...                         ...                    ...         ...
## AH113975 AHLRBaseDbs/v006/LRB.. https://github.com/r..         CSV
## AH113976 AHLRBaseDbs/v006/LRB.. https://github.com/r..         CSV
## AH113977 AHLRBaseDbs/v006/LRB.. https://github.com/r..         CSV
## AH113978 AHLRBaseDbs/v006/LRB.. https://github.com/r..         CSV
## AH113979 AHLRBaseDbs/v006/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 version 4.3.1 (2023-06-16)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.3 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.18-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] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] AnnotationHub_3.9.2 BiocFileCache_2.9.1 dbplyr_2.3.4       
## [4] BiocGenerics_0.47.0 BiocStyle_2.29.2   
## 
## loaded via a namespace (and not attached):
##  [1] KEGGREST_1.41.4               xfun_0.40                    
##  [3] bslib_0.5.1                   Biobase_2.61.0               
##  [5] bitops_1.0-7                  vctrs_0.6.4                  
##  [7] tools_4.3.1                   generics_0.1.3               
##  [9] stats4_4.3.1                  curl_5.1.0                   
## [11] tibble_3.2.1                  fansi_1.0.5                  
## [13] AnnotationDbi_1.63.2          RSQLite_2.3.1                
## [15] blob_1.2.4                    pkgconfig_2.0.3              
## [17] S4Vectors_0.39.3              GenomeInfoDbData_1.2.10      
## [19] lifecycle_1.0.3               compiler_4.3.1               
## [21] Biostrings_2.69.2             GenomeInfoDb_1.37.6          
## [23] httpuv_1.6.11                 htmltools_0.5.6.1            
## [25] sass_0.4.7                    RCurl_1.98-1.12              
## [27] yaml_2.3.7                    interactiveDisplayBase_1.39.0
## [29] pillar_1.9.0                  later_1.3.1                  
## [31] crayon_1.5.2                  jquerylib_0.1.4              
## [33] ellipsis_0.3.2                cachem_1.0.8                 
## [35] mime_0.12                     tidyselect_1.2.0             
## [37] digest_0.6.33                 purrr_1.0.2                  
## [39] dplyr_1.1.3                   bookdown_0.35                
## [41] BiocVersion_3.18.0            fastmap_1.1.1                
## [43] cli_3.6.1                     magrittr_2.0.3               
## [45] utf8_1.2.3                    withr_2.5.1                  
## [47] filelock_1.0.2                promises_1.2.1               
## [49] rappdirs_0.3.3                bit64_4.0.5                  
## [51] rmarkdown_2.25                XVector_0.41.1               
## [53] httr_1.4.7                    bit_4.0.5                    
## [55] png_0.1-8                     memoise_2.0.1                
## [57] shiny_1.7.5.1                 evaluate_0.22                
## [59] knitr_1.44                    IRanges_2.35.3               
## [61] rlang_1.1.1                   Rcpp_1.0.11                  
## [63] xtable_1.8-4                  glue_1.6.2                   
## [65] DBI_1.1.3                     BiocManager_1.30.22          
## [67] jsonlite_1.8.7                R6_2.5.1                     
## [69] zlibbioc_1.47.0