Mercurial > repos > prog > lcmsmatching

annotate massdb-helper.R @ 2:9a0288561ba3 draft

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planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 476a081c0da66822f4e77070f5ce59d9f14511f4-dirty
author prog
date Thu, 02 Mar 2017 11:09:37 -0500
parents 45e985cd8e9e
children
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45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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1 simplifySpectrum <- function(spec) {
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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2 if(length(spec) == 0){
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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3 return(NA_real_)
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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4 }
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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5 #print(spec)
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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6 if (nrow(spec) == 0)
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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7 return(NA_real_)
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8 if (ncol(spec) != 2) {
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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9 spec[, BIODB.PEAK.MZ]
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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10 mint <- BIODB.GROUP.INTENSITY %in% colnames(spec)
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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11 pint <- which(mint[1])
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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12 if (length(pint) == 0)
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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13 stop(
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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14 "No intensity column founds, if there is more than 2 column, columns should be named",
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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15 paste0(BIODB.GROUP.INTENSITY, collapse = ", ")
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16 )
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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17 spec <- spec[, c(BIODB.PEAK.MZ, BIODB.GROUP.INTENSITY[pint[1]])]
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18 ###Normalizing the intenities.
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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19 }
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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20 spec[, 2] <- as.numeric(spec[, 2]) * 100 / max(as.numeric(spec[, 2]))
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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21 colnames(spec) <- c(BIODB.PEAK.MZ, BIODB.PEAK.RELATIVE.INTENSITY)
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22 spec
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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23 }
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24
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25
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26
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27 calcDistance <-
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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28 function(spec1 ,
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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29 spec2,
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30 npmin = 2,
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31 fun = c("wcosine"),
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32 params = list()) {
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33 #fun <- match.arg(fun)
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34
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35 #SPec are always notmlized in pourcentage toa voir issues;
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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36 spec1 <- simplifySpectrum(spec1)
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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37 spec2 <- simplifySpectrum(spec2)
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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38 if(is.na(spec1)||is.na(spec2)) return(list(matched=numeric(0),similarity=0))
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39 params$mz1 <- as.numeric(spec1[, BIODB.PEAK.MZ])
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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40 params$mz2 <- as.numeric(spec2[, BIODB.PEAK.MZ])
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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41 params$int1 <- as.numeric(spec1[, BIODB.PEAK.RELATIVE.INTENSITY])
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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42 params$int2 <- as.numeric(spec2[, BIODB.PEAK.RELATIVE.INTENSITY])
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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43 res <- do.call(fun, args = params)
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44 if (sum(res$matched != -1) < npmin)
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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45 return(list(matched = res$matched, similarity = 0))
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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46 list(matched = res$matched,
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47 similarity = res$measure)
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48 }
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49
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50
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51
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52 ###The returned sim list is not ordered
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53 compareSpectra <-
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54 function(spec,
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55 libspec,
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56 npmin = 2,
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57 fun = BIODB.MSMS.DIST.WCOSINE,
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58 params = list(),
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59 decreasing = TRUE) {
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60 #fun <- match.arg(fun)
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61 if (length(libspec) == 0) {
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62 return(NULL)
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63 }
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64 if (nrow(spec) == 0) {
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65 return(NULL)
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66 }
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67
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68 ####spec is directly normalized.
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69 vall <-
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70 sapply(
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71 libspec,
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72 calcDistance,
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73 spec1 = spec,
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74 params = params,
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75 fun = fun,
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76 simplify = FALSE
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77 )
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78 ####the list is ordered with the chosen metric.
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79 sim <-
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80 vapply(vall,
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81 '[[',
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82 i = "similarity",
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83 FUN.VALUE = ifelse(decreasing, 0, 1))
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84 osim <- order(sim, decreasing = decreasing)
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85 matched <- sapply(vall, '[[', i = "matched", simplify = FALSE)
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86
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87 return(list(
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88 ord = osim,
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89 matched = matched,
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90 similarity = sim
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91 ))
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92 }