gatherInfo {flagme} | R Documentation |
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.
gatherInfo(pD, obj, newind = NULL, method = c("apex"), findmzind = TRUE, useTIC = FALSE, top = NULL, intensity.cut = 0.05)
pD |
a |
obj |
either a |
newind |
list giving the |
method |
method used to gather abundance information, only |
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 |
intensity.cut |
percentage of the maximum intensity |
This procedure loops through the the table of matched peaks and gathers the
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 |
Mark Robinson
Mark D Robinson (2008). Methods for the analysis of gas chromatography - mass spectrometry data PhD dissertation University of Melbourne.
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)