rtncGTW,ncGTWwarp-method {ncGTW} | R Documentation |
Accessors to the realigned RT and the peaks with adjusted RT of ncGTW alignment.
## S4 method for signature 'ncGTWwarp' rtncGTW(object) ## S4 method for signature 'ncGTWwarp' ncGTWpeaks(object)
object |
a |
rtncGTW
returns a list of the same length as the sample
number, in which each element is a vector of the realigned RT of the
corresponding sample.
rtncGTW
returns a matrix containing peak data with adjusted
RT.
# 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 <- initncGTWparam() # run ncGTW alignment ncGTWoutputs <- vector('list', length(ncGTWinputs)) ncGTWoutputs[[1]] <- ncGTWalign(ncGTWinputs[[1]], xcmsLargeWin, 5, ncGTWparam = ncGTWparam) # adjust RT with the realignment results from ncGTW ncGTWres <- xcmsLargeWin adjustRes <- adjustRT(ncGTWres, ncGTWinputs[[1]], ncGTWoutputs[[1]], ppm) rt <- rtncGTW(adjustRes) peaks <- ncGTWpeaks(adjustRes) ## End(Not run)