idMSMStoMSP-data: Example data for 'MetCirc': 'finalMSP'

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

Description

finalMSP is of instance MSP, a container for MS/MS data. finalMSP is derived from the object tissue and compartmentTissue.

Usage

finalMSP

Format

object of class MSP

Value

object of class MSP

Author(s)

Thomas Naake, [e-mail]

Source

data("idMSMStissueproject", package = "MetCirc") ## create vectors with precursor names present in tissue 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, rt = TRUE) finalMSP <- combine(finalMSP, convert2MSP(tissueLIM), rt = TRUE) finalMSP <- combine(finalMSP, convert2MSP(tissueANT), rt = TRUE) finalMSP <- combine(finalMSP, convert2MSP(tissueSTY), rt = TRUE)

## write finalMSP to idMSMStoMSP.RData save(finalMSP, file = "idMSMStoMSP.RData", compress = "xz")

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