inst/unitTests/testQueries.R

In jotsetung/mirtarbase: mirtarbase: a database of validated miRNA target gene interactions

## can we use regexp???
## no way! they would have to be registered using the sqlite3_create_function
## which doesn't seem to be accessible through RSQLite.
## example; http://www.blackdogfoundry.com/blog/supporting-regular-expressions-in-sqlite/
## dbGetQuery(dbconn(mirtarbase), "select * from mirtarbase limit 3")
## dbGetQuery(dbconn(mirtarbase), "select * from mirtarbase where target_gene regexp '^DUS'")


## We're not testing anything specific here, just trying to get no error.
test_unsorted <- function(){
    library(RSQLite)
    SF <- SpeciesFilter("Mus musculus")
    SF
    Q <- mirtarbase:::.buildQuery(mirtarbase,
                                  columns = listColumns(mirtarbase, "mirtarbase"),
                                  filter=list(SF))
    Q
    tmp <- dbGetQuery(dbconn(mirtarbase), Q)
    head(tmp)
    nrow(tmp)


    ## do something more specific: get all for hsa-miR-16-5p.
    F <- MatMirnaFilter("hsa-miR-16-5p")
    cls <- listColumns(mirtarbase, "mirtarbase")
    Res <- mirtarbase:::.getWhat(mirtarbase, filter=list(F), columns = cls)
    nrow(Res)

    ## well ... way too many...
    F <- GenenameFilter("BCL2L11")
    Res <- mirtarbase:::.getWhat(mirtarbase, filter=list(F), columns = cls)
    nrow(Res)
    Res
    ## as we see, the query is performed case insensitive! If we don't want that
    ## we have to say match.case=TRUE
    Res <- mirtarbase:::.getWhat(mirtarbase, filter=list(F), match.case=TRUE,
                                 columns = cls)
    nrow(Res)
    Res
    ## or restrict to human genes only would also do it...
    Res <- mirtarbase:::.getWhat(mirtarbase,
                                 filter=list(F,
                                             SpeciesFilter("Homo sapiens",
                                                           feature="gene")),
                                 order.by="mirna", columns = cls)
    nrow(Res)
    Res
    ## we get now however duplicated miRNA-target gene pairs, one for each publication
    ## in which the MTI was validated


    ## check the performance of mclapply vs normal apply...
    ## 10 rows
    Res <- dbGetQuery(dbconn(mirtarbase),
                      "select * from mirtarbase order by mirtarbase_id limit 10")
    system.time(
        bli <- mirtarbase:::data.frame2mti(Res)
    )
    ## 0.008
    system.time(
        bla <- mirtarbase:::data.frame2mtiNreport(Res)
    )
    ## 0.016
    ## check if it makes sense:
    Res[ Res$mirtarbase_id=="MIRT000006", ]
    bla[["MIRT000006"]]
    ## Perfectly fine!!!


    ## 50 rows:
    Res <- dbGetQuery(dbconn(mirtarbase),
                      "select * from mirtarbase order by mirtarbase_id limit 50")
    system.time(
        bli <- mirtarbase:::data.frame2mti(Res)
    )
    ## 0.024
    system.time(
        bla <- mirtarbase:::data.frame2mtiNreport(Res)
    )
    ## 0.077


    ## 100 rows:
    Res <- dbGetQuery(dbconn(mirtarbase),
                      "select * from mirtarbase order by mirtarbase_id limit 100")
    system.time(
        bli <- mirtarbase:::data.frame2mti(Res)
    )
    ## 0.039
    system.time(
        bla <- mirtarbase:::data.frame2mtiNreport(Res)
    )
    ## 0.151


    ## 400 rows:
    Res <- dbGetQuery(dbconn(mirtarbase),
                      "select * from mirtarbase order by mirtarbase_id limit 400")
    system.time(
        bli <- mirtarbase:::data.frame2mti(Res)
    )
    ## 0.150
    system.time(
        bla <- mirtarbase:::data.frame2mtiNreport(Res)
    )
    ## 0.526


    ## 1000 rows:
    Res <- dbGetQuery(dbconn(mirtarbase),
                      "select * from mirtarbase order by mirtarbase_id limit 1000")
    system.time(
        bli <- mirtarbase:::data.frame2mti(Res)
    )
    ## 0.395
    system.time(
        bla <- mirtarbase:::data.frame2mtiNreport(Res)
    )
    ## 1.369

    Test <- bli[[1]]



    ##*********************************************************
    ##
    ##  Testing conversion functions
    ##
    ##*********************************************************
    ## pre-miRNA to mature miRNA
    Res <- premirna2matmirna(c("bla", "hsa-mir-16-1", "hsa-mir-15b",
                               "hsa-mir-16-2"), return.type="list")
    Res
    Res <- premirna2matmirna(c("bla", "hsa-mir-16-1", "hsa-mir-15b",
                               "hsa-mir-16-2", "hsa-mir-16-1"))
    Res
    Res <- premirna2matmirnaAcc(c("hsa-mir-15b"))
    Res
    Res <- premirnaAcc2matmirna(c("MI0000070"))
    Res
    Res <- premirnaAcc2matmirnaAcc(c("MI0000070"))
    Res
    Res <- premirna2premirnaAcc("hsa-mir-15b")
    Res
    Res <- premirnaAcc2premirna("MI0000070")
    Res

    ## mature miRNA to pre-miRNA
    Res <- matmirna2premirna(c("hsa-miR-16-5p", "hsa-miR-16-3p",
                               "hsa-miR-16-1-3p"))
    Res
    Res <- matmirna2premirnaAcc(c("hsa-miR-16-5p", "hsa-miR-16-3p"))
    Res
    Res <- matmirnaAcc2premirna(c("MIMAT0000069", "MIMAT0004489"))
    Res
    Res <- matmirnaAcc2premirnaAcc("MIMAT0004489")
    Res
    Res <- matmirna2matmirnaAcc("hsa-miR-16-5p")
    Res
    Res <- matmirnaAcc2matmirna("MIMAT0004489")
    Res

    ## pre-miRNA to mirfam and vice versa
    Res <- premirna2mirfam(c("hsa-mir-16-1", "hsa-mir-15b", "hsa-mir-16-2",
                             "hsa-mir-15b"))
    Res
    Res <- premirnaAcc2mirfam("MI0000070")
    Res
    Res <- mirfam2premirna("mir-15")
    head(Res)
    Res <- mirfam2premirnaAcc("mir-15")
    head(Res)
    Res <- mirfam2mirfamAcc("mir-15")
    Res
    Res <- mirfamAcc2mirfam("MIPF0000006")
    Res
    Res <- mirfamAcc2premirna("MIPF0000006")
    head(Res)


    ## mature miRNAs to mirfam and vice versa
    Res <- matmirna2mirfam("hsa-miR-15b-5p")
    Res
    Res <- matmirna2mirfamAcc(c("bla", "hsa-miR-15b-5p"))
    Res
    Res <- mirfam2matmirna("mir-15")   ## weird to get only a handful of mature miRNAs...
    head(Res)
    Res <- mirfamAcc2matmirna("MIPF0000006")
    head(Res)
    Res <- mirfam2matmirnaAcc("mir-15")
    head(Res)
}