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comparison msdb-common.R @ 4:1ba222315fd5 draft

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planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb
author prog
date Thu, 16 Mar 2017 05:05:55 -0400
parents 45e985cd8e9e
children b8f70d8216b3
comparison
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3:abfba8eb1c8d 4:1ba222315fd5
44 # Authorized mz tolerance unit values 44 # Authorized mz tolerance unit values
45 MSDB.MZTOLUNIT.PPM <- 'ppm' 45 MSDB.MZTOLUNIT.PPM <- 'ppm'
46 MSDB.MZTOLUNIT.PLAIN <- 'plain' # same as mz: mass-to-charge ratio 46 MSDB.MZTOLUNIT.PLAIN <- 'plain' # same as mz: mass-to-charge ratio
47 MSDB.MZTOLUNIT.VALS <- c(MSDB.MZTOLUNIT.PPM, MSDB.MZTOLUNIT.PLAIN) 47 MSDB.MZTOLUNIT.VALS <- c(MSDB.MZTOLUNIT.PPM, MSDB.MZTOLUNIT.PLAIN)
48 48
49 # Authorized rt units
50 MSDB.RTUNIT.SEC <- 's'
51 MSDB.RTUNIT.MIN <- 'min'
52 MSDB.RTUNIT.VALS <- c(MSDB.RTUNIT.SEC ,MSDB.RTUNIT.MIN)
53
49 # Default values 54 # Default values
50 MSDB.DFT.PREC <- list() 55 MSDB.DFT.PREC <- list()
51 MSDB.DFT.PREC[[MSDB.TAG.POS]] <- c("[(M+H)]+", "[M+H]+", "[(M+Na)]+", "[M+Na]+", "[(M+K)]+", "[M+K]+") 56 MSDB.DFT.PREC[[MSDB.TAG.POS]] <- c("[(M+H)]+", "[M+H]+", "[(M+Na)]+", "[M+Na]+", "[(M+K)]+", "[M+K]+")
52 MSDB.DFT.PREC[[MSDB.TAG.NEG]] <- c("[(M-H)]-", "[M-H]-", "[(M+Cl)]-", "[M+Cl]-") 57 MSDB.DFT.PREC[[MSDB.TAG.NEG]] <- c("[(M-H)]-", "[M-H]-", "[(M+Cl)]-", "[M+Cl]-")
53 MSDB.DFT.OUTPUT.FIELDS <- list( mz = 'mz', rt = 'rt', col = 'col', colrt = 'colrt', molid = 'id', attr = 'attribution', comp = 'composition', int = 'intensity', rel = 'relative', mzexp = 'mzexp', mztheo = 'mztheo', msmatching = 'msmatching', molnames = 'molnames', molcomp = 'molcomp', molmass = 'molmass', inchi = 'inchi', inchikey = 'inchikey', pubchem = 'pubchem', chebi = 'chebi', hmdb = 'hmdb', kegg = 'kegg') 58 MSDB.DFT.OUTPUT.FIELDS <- list( mz = 'mz', rt = 'rt', col = 'col', colrt = 'colrt', molid = 'id', attr = 'attribution', comp = 'composition', int = 'intensity', rel = 'relative', mzexp = 'mzexp', mztheo = 'mztheo', msmatching = 'msmatching', molnames = 'molnames', molcomp = 'molcomp', molmass = 'molmass', inchi = 'inchi', inchikey = 'inchikey', pubchem = 'pubchem', chebi = 'chebi', hmdb = 'hmdb', kegg = 'kegg')