Mercurial > repos > prog > lcmsmatching

comparison MsPeakForestDb.R @ 4:b34c14151f25 draft

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planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 494194bb501d1d7033613131865f7bd68976041c
author prog
date Tue, 14 Mar 2017 12:40:22 -0400
parents f61ce21ed17c
children fb9c0409d85c
comparison
equal deleted inserted replaced
3:f61ce21ed17c 4:b34c14151f25
257 257
258 # Get spectra 258 # Get spectra
259 spectra <- .self$.get.url(url = url) 259 spectra <- .self$.get.url(url = url)
260 260
261 # Build result data frame 261 # Build result data frame
262 results <- data.frame(MSDB.TAG.MOLID = character(), MSDB.TAG.MOLNAMES = character(), MSDB.TAG.MZTHEO = numeric(), MSDB.TAG.COMP = character(), MSDB.TAG.ATTR = character()) 262 results <- data.frame(MSDB.TAG.MOLID = character(), MSDB.TAG.MOLNAMES = character(), MSDB.TAG.MOLMASS = numeric(), MSDB.TAG.MZTHEO = numeric(), MSDB.TAG.COMP = character(), MSDB.TAG.ATTR = character(), MSDB.TAG.INCHI = character(), MSDB.TAG.INCHIKEY = character(), MSDB.TAG.CHEBI = character(), MSDB.TAG.HMDB = character(), MSDB.TAG.KEGG = character(), MSDB.TAG.PUBCHEM = character())
263 for (x in spectra) { 263 for (x in spectra) {
264 if ('source' %in% names(x) && is.list(x$source)) 264 if ('source' %in% names(x) && is.list(x$source))
265 results <- rbind(results, data.frame(MSDB.TAG.MOLID = vapply(x$source$listOfCompounds, function(c) as.character(c$id), FUN.VALUE = ''), 265 mztheo <- if ('theoricalMass' %in% names(x)) as.numeric(x$theoricalMass) else NA_real_
266 MSDB.TAG.MOLNAMES = vapply(x$source$listOfCompounds, function(c) paste(c$names, collapse = MSDB.MULTIVAL.FIELD.SEP), FUN.VALUE = ''), 266 comp <- if ('composition' %in% names(x)) x$composition else NA_character_
267 MSDB.TAG.MZTHEO = as.numeric(x$theoricalMass), 267 attr <- if ('attribution' %in% names(x)) x$attribution else NA_character_
268 MSDB.TAG.COMP = as.character(x$composition), 268 if ('listOfCompounds' %in% names(x$source)) {
269 MSDB.TAG.ATTR = as.character(x$attribution), 269 molids <- vapply(x$source$listOfCompounds, function(c) as.character(c$id), FUN.VALUE = '')
270 stringsAsFactors = FALSE)) 270 molnames <- vapply(x$source$listOfCompounds, function(c) paste(c$names, collapse = MSDB.MULTIVAL.FIELD.SEP), FUN.VALUE = '')
271 mass <- vapply(x$source$listOfCompounds, function(c) as.character(c$averageMass), FUN.VALUE = '')
272 inchi <- vapply(x$source$listOfCompounds, function(c) as.character(c$inChI), FUN.VALUE = '')
273 inchikey <- vapply(x$source$listOfCompounds, function(c) as.character(c$inChIKey), FUN.VALUE = '')
274 chebi <- vapply(x$source$listOfCompounds, function(c) as.character(c$ChEBI), FUN.VALUE = '')
275 chebi[chebi == 'CHEBI:null'] <- NA_character_
276 hmdb <- vapply(x$source$listOfCompounds, function(c) as.character(c$HMDB), FUN.VALUE = '')
277 hmdb[hmdb == 'HMDBnull'] <- NA_character_
278 kegg <- vapply(x$source$listOfCompounds, function(c) as.character(c$KEGG), FUN.VALUE = '')
279 pubchem <- vapply(x$source$listOfCompounds, function(c) as.character(c$PubChemCID), FUN.VALUE = '')
280 if (length(molids) > 0 && length(molids) == length(molnames))
281 results <- rbind(results, data.frame(MSDB.TAG.MOLID = molids, MSDB.TAG.MOLNAMES = molnames, MSDB.TAG.MOLMASS = mass, MSDB.TAG.MZTHEO = mztheo, MSDB.TAG.COMP = comp, MSDB.TAG.ATTR = attr, MSDB.TAG.INCHI = inchi, MSDB.TAG.INCHIKEY = inchikey, MSDB.TAG.CHEBI = chebi, MSDB.TAG.HMDB = hmdb, MSDB.TAG.KEGG = kegg, MSDB.TAG.PUBCHEM = pubchem, stringsAsFactors = FALSE))
282 }
271 } 283 }
272 284
273 # RT search 285 # RT search
274 if ( ! is.null(rt.low) && ! is.null(rt.high)) { 286 if ( ! is.null(rt.low) && ! is.null(rt.high)) {
275 287