Authors: Koki Tsuyuzaki [aut, cre], Manabu Ishii [aut], Itoshi Nikaido [aut]
Last modified: 2022-04-12 12:06:15
Compiled: Thu Apr 21 13:08:33 2022

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 376 records
## # snapshotDate(): 2022-04-21
## # $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)             
##   ...        ...                                                           
##   AH100542 | LRBaseDb for Taeniopygia guttata (Zebra finch, v003)          
##   AH100543 | LRBaseDb for Takifugu rubripes (Fugu, v003)                   
##   AH100544 | LRBaseDb for Ursus maritimus (Polar bear, v003)               
##   AH100545 | LRBaseDb for Vulpes vulpes (Red fox, v003)                    
##   AH100546 | LRBaseDb for Xenopus tropicalis (Tropical clawed frog, v003)

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

mcols(query(ah, "LRBaseDb"))
## DataFrame with 376 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
## ...                         ...                    ...                    ...
## AH100542 LRBaseDb for Taeniop.. FANTOM5,DLRP,IUPHAR,..    Taeniopygia guttata
## AH100543 LRBaseDb for Takifug.. FANTOM5,DLRP,IUPHAR,..      Takifugu rubripes
## AH100544 LRBaseDb for Ursus m.. FANTOM5,DLRP,IUPHAR,..        Ursus maritimus
## AH100545 LRBaseDb for Vulpes .. FANTOM5,DLRP,IUPHAR,..          Vulpes vulpes
## AH100546 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
## ...             ...         ...                    ...                ...
## AH100542      59729          NA Correspondence table..                  1
## AH100543      31033          NA Correspondence table..                  1
## AH100544      29073          NA Correspondence table..                  1
## AH100545       9627          NA Correspondence table..                  1
## AH100546       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
## ...                         ...            ...           ...
## AH100542 Koki Tsuyuzaki <k.t...     2022-04-21   AHLRBaseDbs
## AH100543 Koki Tsuyuzaki <k.t...     2022-04-21   AHLRBaseDbs
## AH100544 Koki Tsuyuzaki <k.t...     2022-04-21   AHLRBaseDbs
## AH100545 Koki Tsuyuzaki <k.t...     2022-04-21   AHLRBaseDbs
## AH100546 Koki Tsuyuzaki <k.t...     2022-04-21   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
## ...                                                   ...         ...
## AH100542                  Annotation,BADERLAB,BIOMART,...  SQLiteFile
## AH100543                  Annotation,BADERLAB,BIOMART,...  SQLiteFile
## AH100544                  Annotation,BADERLAB,BIOMART,...  SQLiteFile
## AH100545                  Annotation,BADERLAB,BIOMART,...  SQLiteFile
## AH100546                  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
## ...                         ...                    ...         ...
## AH100542 AHLRBaseDbs/v003/LRB.. https://github.com/r..         CSV
## AH100543 AHLRBaseDbs/v003/LRB.. https://github.com/r..         CSV
## AH100544 AHLRBaseDbs/v003/LRB.. https://github.com/r..         CSV
## AH100545 AHLRBaseDbs/v003/LRB.. https://github.com/r..         CSV
## AH100546 AHLRBaseDbs/v003/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) (2022-03-10 r81873)
## Platform: x86_64-apple-darwin19.6.0 (64-bit)
## Running under: macOS Catalina 10.15.7
## 
## Matrix products: default
## BLAS:   /Users/ka36530_ca/R-stuff/bin/R-devel/lib/libRblas.dylib
## LAPACK: /Users/ka36530_ca/R-stuff/bin/R-devel/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_3.3.11 BiocFileCache_2.3.4  dbplyr_2.1.1        
## [4] BiocGenerics_0.41.2  BiocStyle_2.23.1    
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.8.3                  png_0.1-7                    
##  [3] Biostrings_2.63.3             assertthat_0.2.1             
##  [5] digest_0.6.29                 utf8_1.2.2                   
##  [7] mime_0.12                     R6_2.5.1                     
##  [9] GenomeInfoDb_1.31.7           stats4_4.2.0                 
## [11] RSQLite_2.2.12                evaluate_0.15                
## [13] httr_1.4.2                    pillar_1.7.0                 
## [15] zlibbioc_1.41.0               rlang_1.0.2                  
## [17] curl_4.3.2                    jquerylib_0.1.4              
## [19] blob_1.2.3                    S4Vectors_0.33.17            
## [21] rmarkdown_2.13                stringr_1.4.0                
## [23] RCurl_1.98-1.6                bit_4.0.4                    
## [25] shiny_1.7.1                   compiler_4.2.0               
## [27] httpuv_1.6.5                  xfun_0.30                    
## [29] pkgconfig_2.0.3               htmltools_0.5.2              
## [31] tidyselect_1.1.2              KEGGREST_1.35.0              
## [33] GenomeInfoDbData_1.2.8        tibble_3.1.6                 
## [35] interactiveDisplayBase_1.33.0 bookdown_0.26                
## [37] IRanges_2.29.1                fansi_1.0.3                  
## [39] crayon_1.5.1                  dplyr_1.0.8                  
## [41] later_1.3.0                   bitops_1.0-7                 
## [43] rappdirs_0.3.3                jsonlite_1.8.0               
## [45] xtable_1.8-4                  lifecycle_1.0.1              
## [47] DBI_1.1.2                     magrittr_2.0.3               
## [49] cli_3.2.0                     stringi_1.7.6                
## [51] cachem_1.0.6                  XVector_0.35.0               
## [53] promises_1.2.0.1              bslib_0.3.1                  
## [55] ellipsis_0.3.2                filelock_1.0.2               
## [57] generics_0.1.2                vctrs_0.4.1                  
## [59] tools_4.2.0                   bit64_4.0.5                  
## [61] Biobase_2.55.2                glue_1.6.2                   
## [63] purrr_0.3.4                   BiocVersion_3.15.2           
## [65] fastmap_1.1.0                 yaml_2.3.5                   
## [67] AnnotationDbi_1.57.1          BiocManager_1.30.16          
## [69] memoise_2.0.1                 knitr_1.38                   
## [71] sass_0.4.1