spectra_tissue: Example data for 'MetCirc': 'spectra_tissue'

In MetCirc: Navigating mass spectral similarity in high-resolution MS/MS metabolomics data

Description

'spectra_tissue' is a 'MSpectra' object containing 'Spectrum2' objects derived from the 'idMSMStissueproject' data set. See the vignette for a workflow to reproduce the object 'spectra'.

Format

'matrix'

Value

'matrix'

Author(s)

Thomas Naake, [e-mail]

Source

data("idMSMStissueproject", package = "MetCirc") ## get all MS/MS spectra tissue <- tissue[tissue[, "id"] id_uniq <- unique(tissue[, "id"])

## obtain precursor m/z from id_uniq prec_mz_l <- lapply(strsplit(as.character(id_uniq), split = "_"), "[", 1) prec_mz_l <- lapply(prec_mz_l, as.numeric)

## obtain m/z from fragments per precursor m/z mz_l <- lapply(id_uniq, function(x) tissue[tissue[, "id"] == x, "mz"]) ## obtain corresponding intensity values int_l <- lapply(id_uniq, function(x) tissue[tissue[, "id"] == x, "intensity"]) ## obtain retention time by averaging all retention time values rt_l <- lapply(id_uniq, function(x) tissue[tissue[, "id"] == x, "rt"]) rt_l <- lapply(rt_l, mean)

## create list of spectrum2 objects spectrum2_tissue <- lapply(1:length(mz_l), function(x) new("Spectrum2", rt = rt_l[[x]], precursorMz = prec_mz_l[[x]], mz = mz_l[[x]], intensity = int_l[[x]]))

## combine list of spectrum2 objects to MSpectra object, ## use SPL, LIM, ANT, STY for further analysis spectra_tissue <- MSpectra(spectrum2_tissue, elementMetadata = DataFrame(compartmentTissue[, c("SPL", "LIM", "ANT", "STY")]))

save(spectra_tissue, file = "spectra.RData", compress = "xz")

MetCirc documentation built on Nov. 8, 2020, 8:26 p.m.