adjustRT {ncGTW} | R Documentation |
This function produces the new warping functions (RT lists) with the realignment result.
adjustRT(xcmsLargeWin, ncGTWinput, ncGTWoutput, ppm)
xcmsLargeWin |
A |
ncGTWinput |
A |
ncGTWoutput |
A |
ppm |
Should be set as same as the one when performing the peak
detection function in |
This function produces the new warping functions (RT lists) with the realignment result.
A ncGTWwarp
object.
# 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)