binnedMSP: Example data for 'MetCirc': 'binnedMSP'

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

Description

The object binnedMSP is a matrix, where rows are metabolites detected in the tissues sepal (SPL), limb (LIM), anther (ANT) and style (STY). The columns contain binned m/z values. Entries contain the intensity (in percent) of a certain metabolite at a certain m/z value. binnedMSP is derived from the object tissue and compartmentTissue.

Usage

binnedMSP

Format

matrix

Value

matrix

Author(s)

Thomas Naake, [e-mail]

Source

data("idMSMStissueproject", package = "MetCirc") data("idMSMStoMSP", package = "MetCirc") tissueSPL <- compartmentTissue[compartmentTissue[,"SPL"] == TRUE, 1] tissueLIM <- compartmentTissue[compartmentTissue[,"LIM"] == TRUE, 1] tissueANT <- compartmentTissue[compartmentTissue[,"ANT"] == TRUE, 1] tissueSTY <- compartmentTissue[compartmentTissue[,"STY"] == TRUE, 1]

## truncate tissue tissueSPL <- tissue[tissue[,4] tissueLIM <- tissue[tissue[,4] tissueANT <- tissue[tissue[,4] tissueSTY <- tissue[tissue[,4]

## create msp and combine msp objects of different tissues finalMSP <- convert2MSP(tissueSPL, splitIndMZ = 1, splitIndRT = 2, rt = TRUE) finalMSP <- combine(finalMSP, convert2MSP(tissueLIM, splitIndRT = 2, rt = TRUE)) finalMSP <- combine(finalMSP, convert2MSP(tissueANT, splitIndRT = 2, rt = TRUE)) finalMSP <- combine(finalMSP, convert2MSP(tissueSTY, splitIndRT = 2, rt = TRUE))

## create vector with compartments compSPL <- rep("SPL", length(convert2MSP(tissueSPL))) compLIM <- rep("LIM", length(convert2MSP(tissueLIM))) compANT <- rep("ANT", length(convert2MSP(tissueANT))) compSTY <- rep("STY", length(convert2MSP(tissueSTY)))

compartment <- c(compSPL, compLIM, compANT, compSTY) binnedMSP <- binning(msp = finalMSP, tol = 0.01, group = compartment, method = "median") save(binnedMSP, file = "binnedMSP.RData", compress = "bzip2")

PlantDefenseMetabolism/MetCirc documentation built on May 8, 2019, 2:52 p.m.