alignData,ncGTWoutput-method {ncGTW} | R Documentation |
Accessors to the alignment information and result by ncGTW.
## S4 method for signature 'ncGTWoutput' alignData(object)
object |
a |
alignData
returns a matrix in which each row is a sample
profile after downsampling.
# 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)) for (n in seq_along(ncGTWinputs)) ncGTWoutputs[[n]] <- ncGTWalign(ncGTWinputs[[n]], xcmsLargeWin, 5, ncGTWparam = ncGTWparam) data <- alignData(ncGTWoutputs[[1]]) rt <- scanRange(ncGTWoutputs[[1]]) paths <- ncGTWpath(ncGTWoutputs[[1]]) downSam <- downSample(ncGTWoutputs[[1]]) ## End(Not run)