adjustRT: Adjust retention time

In ChiungTingWu/ncGTW: Alignment of LC-MS Profiles by Neighbor-wise Compound-specific Graphical Time Warping with Misalignment Detection

Description

This function produces the new warping functions (RT lists) with the realignment result.

Usage

adjustRT(xcmsLargeWin, ncGTWinput, ncGTWoutput, ppm)

Arguments

xcmsLargeWin	A xcmsSet-class object.
ncGTWinput	A ncGTWinput object.
ncGTWoutput	A ncGTWoutput object.
ppm	Should be set as same as the one when performing the peak detection function in xcms.

Details

This function produces the new warping functions (RT lists) with the realignment result.

Value

A ncGTWwarp object.

Examples

# obtain data
data('xcmsExamples')
xcmsLargeWin <- xcmsExamples$xcmsLargeWin
xcmsSmallWin <- xcmsExamples$xcmsSmallWin
ppm <- xcmsExamples$ppm

# detect misaligned features
excluGroups <- misalignDetect(xcmsLargeWin, xcmsSmallWin, ppm)

# obtain the paths of the sample files
filepath <- system.file("extdata", package = "ncGTW")
file <- list.files(filepath, pattern="mzxml", full.names=TRUE)

tempInd <- matrix(0, length(file), 1)
for (n in seq_along(file)){
    tempCha <- file[n]
    tempLen <- nchar(tempCha)
    tempInd[n] <- as.numeric(substr(tempCha, regexpr("example", tempCha) + 7,
        tempLen - 6))
}
# sort the paths by data acquisition order
file <- file[sort.int(tempInd, index.return = TRUE)$ix]
## Not run: 
# load the sample profiles
ncGTWinputs <- loadProfile(file, excluGroups)

# initialize the parameters of ncGTW alignment with default
ncGTWparam <- new("ncGTWparam")

# run ncGTW alignment
ncGTWoutputs <- vector('list', length(ncGTWinputs))
for (n in seq_along(ncGTWinputs))
    ncGTWoutputs[[n]] <- ncGTWalign(ncGTWinputs[[n]], xcmsLargeWin, 5,
        ncGTWparam = ncGTWparam)

# adjust RT with the realignment results from ncGTW
ncGTWres <- xcmsLargeWin
ncGTWRt <- vector('list', length(ncGTWinputs))
for (n in seq_along(ncGTWinputs)){
    adjustRes <- adjustRT(ncGTWres, ncGTWinputs[[n]], ncGTWoutputs[[n]], ppm)
    xcms::peaks(ncGTWres) <- ncGTWpeaks(adjustRes)
    ncGTWRt[[n]] <- rtncGTW(adjustRes)
}

# apply the adjusted RT to a xcmsSet object
xcms::groups(ncGTWres) <- excluGroups[ , 2:9]
xcms::groupidx(ncGTWres) <- xcms::groupidx(xcmsLargeWin)[excluGroups[ , 1]]
rtCor <- vector('list', length(xcms::filepaths(ncGTWres)))
for (n in seq_along(file)){
    rtCor[[n]] <- vector('list', dim(excluGroups)[1])
    for (m in seq_len(dim(excluGroups)[1]))
        rtCor[[n]][[m]] <- ncGTWRt[[m]][[n]]
}
slot(ncGTWres, 'rt')$corrected <- rtCor

## End(Not run)

ChiungTingWu/ncGTW documentation built on Dec. 30, 2019, 10:12 p.m.