Authors: Koki Tsuyuzaki [aut, cre], Manabu Ishii [aut], Itoshi Nikaido [aut]
Last modified: 2021-10-26 08:47:32
Compiled: Tue Oct 26 08:48:05 2021

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 250 records
## # snapshotDate(): 2021-10-20
## # $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)             
##   ...       ...                                                           
##   AH97834 | LRBaseDb for Taeniopygia guttata (Zebra finch, v002)          
##   AH97835 | LRBaseDb for Takifugu rubripes (Fugu, v002)                   
##   AH97836 | LRBaseDb for Ursus maritimus (Polar bear, v002)               
##   AH97837 | LRBaseDb for Vulpes vulpes (Red fox, v002)                    
##   AH97838 | LRBaseDb for Xenopus tropicalis (Tropical clawed frog, v002)

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

mcols(query(ah, "LRBaseDb"))
## DataFrame with 250 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
## ...                        ...                    ...                    ...
## AH97834 LRBaseDb for Taeniop.. FANTOM5,DLRP,IUPHAR,..    Taeniopygia guttata
## AH97835 LRBaseDb for Takifug.. FANTOM5,DLRP,IUPHAR,..      Takifugu rubripes
## AH97836 LRBaseDb for Ursus m.. FANTOM5,DLRP,IUPHAR,..        Ursus maritimus
## AH97837 LRBaseDb for Vulpes .. FANTOM5,DLRP,IUPHAR,..          Vulpes vulpes
## AH97838 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
## ...            ...         ...                    ...                ...
## AH97834      59729          NA Correspondence table..                  1
## AH97835      31033          NA Correspondence table..                  1
## AH97836      29073          NA Correspondence table..                  1
## AH97837       9627          NA Correspondence table..                  1
## AH97838       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
## ...                        ...            ...           ...
## AH97834 Koki Tsuyuzaki <k.t...     2021-10-15   AHLRBaseDbs
## AH97835 Koki Tsuyuzaki <k.t...     2021-10-15   AHLRBaseDbs
## AH97836 Koki Tsuyuzaki <k.t...     2021-10-15   AHLRBaseDbs
## AH97837 Koki Tsuyuzaki <k.t...     2021-10-15   AHLRBaseDbs
## AH97838 Koki Tsuyuzaki <k.t...     2021-10-15   AHLRBaseDbs
##                                                     tags  rdataclass
##                                                   <list> <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
## ...                                                  ...         ...
## AH97834                  Annotation,BADERLAB,BIOMART,...  SQLiteFile
## AH97835                  Annotation,BADERLAB,BIOMART,...  SQLiteFile
## AH97836                  Annotation,BADERLAB,BIOMART,...  SQLiteFile
## AH97837                  Annotation,BADERLAB,BIOMART,...  SQLiteFile
## AH97838                  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
## ...                        ...                    ...         ...
## AH97834 AHLRBaseDbs/v002/LRB.. https://github.com/r..         CSV
## AH97835 AHLRBaseDbs/v002/LRB.. https://github.com/r..         CSV
## AH97836 AHLRBaseDbs/v002/LRB.. https://github.com/r..         CSV
## AH97837 AHLRBaseDbs/v002/LRB.. https://github.com/r..         CSV
## AH97838 AHLRBaseDbs/v002/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 4.1.1 Patched (2021-10-13 r81052)
## Platform: x86_64-apple-darwin17.7.0 (64-bit)
## Running under: macOS Catalina 10.15.7
## 
## Matrix products: default
## BLAS:   /Users/ka36530_ca/R-stuff/bin/R-4-1/lib/libRblas.dylib
## LAPACK: /Users/ka36530_ca/R-stuff/bin/R-4-1/lib/libRlapack.dylib
## 
## locale:
## [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] AnnotationHub_3.1.6 BiocFileCache_2.1.1 dbplyr_2.1.1       
## [4] BiocGenerics_0.39.2 BiocStyle_2.21.4   
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.7                    png_0.1-7                    
##  [3] Biostrings_2.61.2             assertthat_0.2.1             
##  [5] digest_0.6.28                 utf8_1.2.2                   
##  [7] mime_0.12                     R6_2.5.1                     
##  [9] GenomeInfoDb_1.29.10          stats4_4.1.1                 
## [11] RSQLite_2.2.8                 evaluate_0.14                
## [13] httr_1.4.2                    pillar_1.6.4                 
## [15] zlibbioc_1.39.0               rlang_0.4.12                 
## [17] curl_4.3.2                    jquerylib_0.1.4              
## [19] blob_1.2.2                    S4Vectors_0.31.5             
## [21] rmarkdown_2.11                stringr_1.4.0                
## [23] RCurl_1.98-1.5                bit_4.0.4                    
## [25] shiny_1.7.1                   compiler_4.1.1               
## [27] httpuv_1.6.3                  xfun_0.27                    
## [29] pkgconfig_2.0.3               htmltools_0.5.2              
## [31] tidyselect_1.1.1              KEGGREST_1.33.0              
## [33] GenomeInfoDbData_1.2.7        tibble_3.1.5                 
## [35] interactiveDisplayBase_1.31.2 bookdown_0.24                
## [37] IRanges_2.27.2                fansi_0.5.0                  
## [39] withr_2.4.2                   crayon_1.4.1                 
## [41] dplyr_1.0.7                   later_1.3.0                  
## [43] bitops_1.0-7                  rappdirs_0.3.3               
## [45] jsonlite_1.7.2                xtable_1.8-4                 
## [47] lifecycle_1.0.1               DBI_1.1.1                    
## [49] magrittr_2.0.1                stringi_1.7.5                
## [51] cachem_1.0.6                  XVector_0.33.0               
## [53] promises_1.2.0.1              bslib_0.3.1                  
## [55] ellipsis_0.3.2                filelock_1.0.2               
## [57] generics_0.1.0                vctrs_0.3.8                  
## [59] tools_4.1.1                   bit64_4.0.5                  
## [61] Biobase_2.53.0                glue_1.4.2                   
## [63] purrr_0.3.4                   BiocVersion_3.14.0           
## [65] fastmap_1.1.0                 yaml_2.2.1                   
## [67] AnnotationDbi_1.55.2          BiocManager_1.30.16          
## [69] memoise_2.0.0                 knitr_1.36                   
## [71] sass_0.4.0