spectra_tissue {MetCirc} | R Documentation

## Example data for `MetCirc`: `spectra_tissue`

### Description

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

### Usage

    similarityMat

### Format

`matrix`

### Value

`matrix`

### Author(s)

Thomas Naake, thomasnaake@googlemail.com

### 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 Spectra object, ## use SPL, LIM, ANT, STY for further analysis spectra_tissue <- Spectra(spectrum2_tissue, elementMetadata=DataFrame(compartmentTissue[, c("SPL", "LIM", "ANT", "STY")]))

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

[Package MetCirc version 1.18.0 Index]