create_database: Create database deprecated

In msPurity: Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics

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.rds",
                          package="msPurity"))
xset <- readRDS(system.file("extdata","tests", "xcms",
                            "msms_only_xset.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)

msPurity documentation built on Jan. 14, 2021, 2:44 a.m.