ncGTWoutput-accessors: ncGTWoutput-accessors

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

Description

Accessors to the alignment information and result by ncGTW.

Usage

## S4 method for signature 'ncGTWoutput'
alignData(object)

Arguments

object

a ncGTWoutput object.

Value

alignData returns a matrix in which each row is a sample profile after downsampling.

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 <- 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)

ncGTW documentation built on Nov. 8, 2020, 8:08 p.m.