MPO_vignette

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
## BiocManager::install("BiocUpgrade") ## you may need this
BiocManager::install("MPO.db")

library(MPO.db)
#> MPO.db version 0.99.7

library(AnnotationDbi)
#> Loading required package: stats4
#> Loading required package: BiocGenerics
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#>     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
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#> Loading required package: Biobase
#> Welcome to Bioconductor
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#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
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ls("package:MPO.db")
#>  [1] "MPO"          "MPO.db"       "MPOALIAS"     "MPOANATOMY"   "MPOANCESTOR" 
#>  [6] "MPOCHILDREN"  "MPOMAPCOUNTS" "MPOMGIDO"     "MPOMPDO"      "MPOMPMGI"    
#> [11] "MPOOFFSPRING" "MPOPARENTS"   "MPOSYNONYM"   "MPOTERM"      "MPO_dbInfo"  
#> [16] "MPO_dbconn"   "MPO_dbfile"   "MPO_dbschema" "MPOmetadata"  "columns"     
#> [21] "keys"         "keytypes"     "select"
packageVersion("MPO.db")
#> [1] '0.99.7'

toTable(MPOmetadata)
#>              name
#> 1        DBSCHEMA
#> 2 DBSCHEMAVERSION
#> 3   MPOSOURCENAME
#> 4     MPOSOURCURL
#> 5   MPOSOURCEDATE
#> 6         Db type
#>                                                               value
#> 1                                                            MPO_DB
#> 2                                                               1.0
#> 3                                                               MGI
#> 4 http://www.informatics.jax.org/downloads/reports/index.html#pheno
#> 5                                                          20230302
#> 6                                                             MPODb
MPOMAPCOUNTS
#>  MPOANCESTOR  MPOCHILDREN MPOOFFSPRING   MPOPARENTS      MPOTERM 
#>     "119177"      "17358"     "119177"      "17358"      "13708"

doterm <- toTable(MPOTERM)
head(doterm)
#>         mpid                                  term
#> 1 MP:0000001                   mammalian phenotype
#> 2 MP:0000003    abnormal adipose tissue morphology
#> 3 MP:0000005 increased brown adipose tissue amount
#> 4 MP:0000008 increased white adipose tissue amount
#> 5 MP:0000010 abnormal abdominal fat pad morphology
#> 6 MP:0000013  abnormal adipose tissue distribution

dotermlist <- as.list(MPOTERM)
head(dotermlist)
#> $`MP:0000001`
#> [1] "mammalian phenotype"
#> 
#> $`MP:0000003`
#> [1] "abnormal adipose tissue morphology"
#> 
#> $`MP:0000005`
#> [1] "increased brown adipose tissue amount"
#> 
#> $`MP:0000008`
#> [1] "increased white adipose tissue amount"
#> 
#> $`MP:0000010`
#> [1] "abnormal abdominal fat pad morphology"
#> 
#> $`MP:0000013`
#> [1] "abnormal adipose tissue distribution"

doalias <- as.list(MPOALIAS)
doalias[['MP:0000003']]
#> [1] "MP:0000011"

dosynonym <- as.list(MPOSYNONYM)
dosynonym[['MP:0000003']]
#> [1] "\"abnormality of adipose tissue\" BROAD []"
#> [2] "\"adipose tissue abnormalities\" BROAD []" 
#> [3] "\"adipose tissue dysplasia\" EXACT []"

sessionInfo()
#> R version 4.3.0 RC (2023-04-18 r84287)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 22.04.2 LTS
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#> BLAS:   /home/biocbuild/bbs-3.18-bioc/R/lib/libRblas.so 
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#> [1] AnnotationDbi_1.63.1 IRanges_2.35.1       S4Vectors_0.39.1    
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#> [63] BiocManager_1.30.20           jsonlite_1.8.4               
#> [65] R6_2.5.1                      zlibbioc_1.47.0