Correct gaps in data

Fixes gaps in data due to calibration scans or lock mass. Automatically detects file type and calls the relevant method. The mzXML file keeps the data the same length in time but overwrites the lock mass scans. The netCDF version adds the scans back into the data thereby increasing the length of the data and correcting for the unseen gap.

Methods

object = "xcmsRaw"

stitch(object, lockMass=numeric())

object = "xcmsRaw"

makeacqNum(object, freq=numeric(), start=1)

Arguments

object

An xcmsRaw-class object

lockMass

A dataframe of locations of the gaps

freq

The intervals of the lock mass scans

start

The starting lock mass scan location, default is 1

Details

makeacqNum takes locates the gap using the starting lock mass scan and it's intervals. This data frame is then used in stitch to correct for the gap caused by the lock mass. Correction works by using scans from either side of the gap to fill it in.

Value

stitch A corrected xcmsRaw-class object

makeacqNum A numeric vector of scan locations corresponding to lock Mass scans

Author

Paul Benton, hpaul.benton08@imperial.ac.uk

Examples

if (FALSE) library(xcms)
    library(faahKO)
    ## These files do not have this problem to correct for but just
    ## for an example
    cdfpath <- system.file("cdf", package = "faahKO")
    cdffiles <- list.files(cdfpath, recursive = TRUE, full.names = TRUE)
    xr<-xcmsRaw(cdffiles[1])
#> Create profile matrix with method 'bin' and step 1 ... 
#> OK
    xr
#> An "xcmsRaw" object with 1278 mass spectra
#> 
#> Time range: 2501.4-4499.8 seconds (41.7-75 minutes)
#> Mass range: 200-600 m/z
#> Intensity range: 70-1373180 
#> 
#> MSn data on  0  mass(es)
#> 	with  0  MSn spectra
#> Profile method: bin 
#> Profile step: 1 m/z (401 grid points from 200 to 600 m/z)
#> 
#> Memory usage: 10.8 MB
    ##Lets assume that the lockmass starts at 1 and is every 100 scans
    lockMass<-xcms:::makeacqNum(xr, freq=100, start=1)
    ## these are equcal
    lockmass<-AutoLockMass(xr)
#> Warning: 
#> Lock mass frequency wasn't detected
    ob<-stitch(xr, lockMass)
    ob
#> An "xcmsRaw" object with 1304 mass spectra
#> 
#> Time range: 1.6-2040.7 seconds (0-34 minutes)
#> Mass range: 200-600 m/z
#> Intensity range: 70-1373180 
#> 
#> MSn data on  0  mass(es)
#> 	with  0  MSn spectra
#> Profile method: bin 
#> Profile step: no profile data
#> 
#> Memory usage: 6.96 MB

    ## plot the old data before correction
    foo<-rawEIC(xr, m=c(200,210), scan=c(80,140))
    plot(foo$scan, foo$intensity, type="h")


    ## plot the new corrected data to see what changed
    foo<-rawEIC(ob, m=c(200,210), scan=c(80,140))
    plot(foo$scan, foo$intensity, type="h")