groupInfo,ncGTWinput-method {ncGTW} | R Documentation |
Accessors to the feature and profiles loaded by loadProfile
.
## 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)
object |
a |
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.
# 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)