gatherInfo: Gathers abundance informations from an alignment

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

Gathers abundance informations from an alignment

Description

Given an alignment table (indices of matched peaks across several samples) such as that within a progressiveAlignment or multipleAlignment object, this routines goes through the raw data and collects the abundance of each fragment peak, as well as the retention times across the samples.

Usage

gatherInfo(
  pD,
  obj,
  newind = NULL,
  method = c("apex"),
  findmzind = TRUE,
  useTIC = FALSE,
  top = NULL,
  intensity.cut = 0.05
)

Arguments

pD	a peaksDataset object, to get the abundance data from
obj	either a multipleAlignment or progressiveAlignment object
newind	list giving the
method	method used to gather abundance information, only apex implemented currently.
findmzind	logical, whether to take a subset of all m/z indices
useTIC	logical, whether to use total ion current for abundance summaries
top	only use the top top peaks
intensity.cut	percentage of the maximum intensity

Details

This procedure loops through the the table of matched peaks and gathers the

Value

Returns a list (of lists) for each row in the alignment table. Each list has 3 elements:

mz	a numerical vector of the m/z fragments used
rt	a numerical vector for the exact retention time of each peak across all samples
data	matrix of fragment intensities. If useTIC = TRUE, this matrix will have a single row

Author(s)

Mark Robinson

References

Mark D Robinson (2008). Methods for the analysis of gas chromatography - mass spectrometry data PhD dissertation University of Melbourne.

See Also

imputePeaks

Examples

  require(gcspikelite)

  ## paths and files
  gcmsPath <- paste(find.package("gcspikelite"), "data", sep = "/")
  cdfFiles <- dir(gcmsPath, "CDF", full = TRUE)
  eluFiles <- dir(gcmsPath, "ELU", full = TRUE)

  ## read data, peak detection results
  pd <- peaksDataset(cdfFiles[1:2], mz = seq(50, 550), rtrange = c(7.5, 8.5))
  pd <- addAMDISPeaks(pd, eluFiles[1:2])

  ## multiple alignment
  ma <- multipleAlignment(pd, c(1,1), wn.gap = 0.5, wn.D = 0.05, bw.gap = 0.6, 
                          bw.D = 0.2, usePeaks = TRUE, filterMin = 1, df = 50,
                          verbose = TRUE, metric = 1, type = 1)

  ## gather apex intensities
  d <- gatherInfo(pd, ma)

  ## table of retention times
  nm <- list(paste("MP", 1:length(d), sep = ""), c("S1", "S2"))
  rts <- matrix(unlist(sapply(d, .subset, "rt")), byrow = TRUE, nc = 2, 
                dimnames = nm)

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