ncGTWinput-accessors: ncGTWinput-accessors

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

Description

Accessors to the feature and profiles loaded by loadProfile.

Usage

## S4 method for signature 'ncGTWinput'
groupInfo(object)

## S4 method for signature 'ncGTWinput'
profiles(object)

## S4 method for signature 'ncGTWinput'
rtRaw(object)

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

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

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

Arguments

object

a ncGTWinput object.

Value

groupInfo returns a vector of the information of the loaded feature.

profiles returns a raw data matrix in which each row is a sample profile.

rtRaw returns a raw RT matrix in which each row is the corresponding sample RT.

scanRange returns a downsampled RT matrix in which each row is the corresponding sample RT in data.

ncGTWpath returns a list of the same length as the sample number, in which each element is a matrix of the alignment result of the corresponding sample.

downSample returns the factor of downsampling when perform ncGTW alignment.

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)

gInfo <- groupInfo(ncGTWinputs[[1]])
prof <- profiles(ncGTWinputs[[1]])
rtR <- rtRaw(ncGTWinputs[[1]])

## End(Not run)

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