loadProfile: Load sample profiles for each peak group

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

Description

This function loads each raw sample profiles from the file with certain m/z and RT range.

Usage

loadProfile(filePaths, excluGroups, mzAdd = 0.005, rtAdd = 10,
  profstep = 0, BPPARAM = BiocParallel::SnowParam(workers = 1))

Arguments

filePaths	The character vector of the loading file paths.
excluGroups	The output matrix of misalignDetect or xcmsSet-class$group, in which mzmin, mzmax, rtmin, and rtmax are set as the m/z and RT range for loading.
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 SerialParam, MulticoreParam, or SnowParam.

Details

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.

Value

A list of the same length as the row number of excluGroups, in which each element is a ncGTWinput 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]

# load the sample profiles
ncGTWinputs <- loadProfile(file, excluGroups)

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