create_database {msPurity} | R Documentation

## Create database deprecated

### Description

Create and SQLite database of an LC-MS(/MS) experiment

msPurity::create_database is deprecated. Please use msPurity::createDatabase for future use

### Usage

    create_database(
      pa,
      xset,
      xsa = NULL,
      out_dir = ".",
      grp_peaklist = NA,
      db_name = NA
    )

### Arguments

`pa` | purityA object; Needs to be the same used for frag4feature function
`xset` | xcms object; Needs to be the same used for frag4feature function (this will be ignored when using xsa parameter)
`xsa` | CAMERA object [optional]; if CAMERA object is used, we ignore the xset parameter input and obtain all information from the xset object nested with the CAMERA xsa object. Adduct and isotope information will be included into the database when using this parameter. The underlying xset object must be the one used for the frag4feature function
`out_dir` | character; Out directory for the SQLite result database
`grp_peaklist` | dataframe [optional]; Can use any peak dataframe. Still needs to be derived from the xset object though
`db_name` | character [optional]; Name of the result database

### Value

path to SQLite database and database name

### Examples

    #msmsPths <- list.files(system.file("extdata", "lcms", "mzML",
    #            package="msPurityData"), full.names = TRUE, pattern = "MSMS")
    #xset <- xcms::xcmsSet(msmsPths)
    #xset <- xcms::group(xset)

    #pa  <- purityA(msmsPths)
    #pa <- frag4feature(pa, xset)
    #pa <- averageAllFragSpectra(pa)
    #db_pth <- create_database(pa, xset)

    # Run from previously generated data
    pa <- readRDS(system.file("extdata", "tests", "purityA",
                              "9_averageAllFragSpectra_with_filter_pa_OLD.rds",
                              package="msPurity"))
    xset <- readRDS(system.file("extdata","tests", "xcms",
                                "msms_only_xset_OLD.rds", package="msPurity"))

    # Need to ensure the filelists are matching
    msmsPths <- list.files(system.file("extdata", "lcms", "mzML",
                                       package="msPurityData"),
                                       full.names = TRUE, pattern = "MSMS")
    pa@fileList[1] <- msmsPths[basename(msmsPths)=="LCMSMS_1.mzML"]
    pa@fileList[2] <- msmsPths[basename(msmsPths)=="LCMSMS_2.mzML"]
    xset@filepaths[1] <- msmsPths[basename(msmsPths)=="LCMSMS_1.mzML"]
    xset@filepaths[2] <- msmsPths[basename(msmsPths)=="LCMSMS_2.mzML"]
    db_pth <- create_database(pa, xset)

[Package msPurity version 1.20.0 Index]