loadProfile {ncGTW} | R Documentation |
This function loads each raw sample profiles from the file with certain m/z and RT range.
loadProfile(filePaths, excluGroups, mzAdd = 0.005, rtAdd = 10, profstep = 0, BPPARAM = BiocParallel::SnowParam(workers = 1))
filePaths |
The character vector of the loading file paths. |
excluGroups |
The output matrix of |
mzAdd |
The extra m/z range for loading (both sides), and the default is 0.005. |
rtAdd |
The extra RT range for loading (both sides), and the default is 10 (seconds). |
profstep |
The size of each m/z bin for peak integration, and the default is 0. |
BPPARAM |
A object of BiocParallel to control parallel processing,
and can be created by
|
This function obtains the extracted ion chromatogram for each sample
at the givin m/z and RT range with a certain m/z bin size for integration.
Considering there may be missing peak by peak detection, mzAdd
and
rtAdd
are to increase the integration range.
A list of the same length as the row number of excluGroups
, in
which each element is a ncGTWinput
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] # load the sample profiles ncGTWinputs <- loadProfile(file, excluGroups)