retFatMatrix: retFatMatrix

In rromoli/flagme: Analysis of Metabolomics GC/MS Data

retFatMatrix

Description

Build a fat data matrix

Usage

retFatMatrix(object, data, minFilter = round(length(object@files)/3 * 2))

Arguments

object	peakDataset object
data	a gatherInfo() object
minFilter	the minimum number for a feature to be returned in the data matrix. Default is 2/3 of the samples

Details

This function allows to extract the data from an object created using gatherInfo and build a data matrix using the area of the deconvoluted and aligned peaks. The row are the samples while the column represent the different peaks.

Value

A fat data matrix containing the area of the deconvoluted and aligned peaks. The row are the samples while the column represent the different peaks

Author(s)

Riccardo Romoli [e-mail]

See Also

gatherInfo

Examples

require(gcspikelite)
files <- list.files(path = paste(find.package("gcspikelite"), "data",
                    sep = "/"),"CDF", full = TRUE)
data <- peaksDataset(files[1:2], mz = seq(50, 550), rtrange = c(7.5, 8.5))
## create settings object
mfp <- xcms::MatchedFilterParam(fwhm = 10, snthresh = 5)
cwt <- xcms::CentWaveParam(snthresh = 3, ppm = 3000, peakwidth = c(3, 40),
 prefilter = c(3, 100), fitgauss = FALSE, integrate = 2, noise = 0,
 extendLengthMSW = TRUE, mzCenterFun = "wMean")
data <- addXCMSPeaks(files[1:2], data, settings = mfp)
data
ma <- multipleAlignment(pd = data, group = c(1,1),
                        filterMin = 1, metric = 2, type = 2)
outList <- gatherInfo(data, ma)
mtxD <- retFatMatrix(object = data, data = outList, minFilter = 1)

rromoli/flagme documentation built on Feb. 10, 2023, 12:59 a.m.