ncGTWalign: Run ncGTW alignment

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

Description

This function applies ncGTW alignment to the input feature.

Usage

ncGTWalign(ncGTWinput, xcmsLargeWin, parSamp = 10, k1Num = 3,
  k2Num = 1, bpParam = BiocParallel::SnowParam(workers = 1),
  ncGTWparam = NULL)

Arguments

ncGTWinput	A ncGTWinput object.
xcmsLargeWin	A xcmsSet-class object.
parSamp	Decide how many samples are in each group when considering parallel computing, and the default is 10.
k1Num	Decide how many different k1 will be tested in stage 1. The default is 3.
k2Num	Decide how many different k2 will be tested in stage 2. The default is 1.
bpParam	A object of BiocParallel to control parallel processing, and can be created by SerialParam, MulticoreParam, or SnowParam.
ncGTWparam	A ncGTWparam object.

Details

This function realign the input feature with ncGTW alignment function with given m/z and RT range.

Value

A ncGTWoutput 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]
## 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)

## End(Not run)

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