stitch-methods: Correct gaps in data

In xiaodfeng/DynamicXCMS: LC-MS and GC-MS Data Analysis

Correct gaps in data

Description

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.

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

Methods

object = "xcmsRaw"

stitch(object, lockMass=numeric())

object = "xcmsRaw"

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

Author(s)

Paul Benton, [e-mail]

Examples

## Not run: 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])
    xr
    ##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)
    ob<-stitch(xr, lockMass)
    ob

    ## 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")

## End(Not run)

xiaodfeng/DynamicXCMS documentation built on Aug. 6, 2023, 3:02 p.m.