Mercurial > repos > computational-metabolomics > mspurity_flagremove

annotate averageFragSpectra.R @ 9:da36e8bbcfbd draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20a48a1862267264f98b7c514287f9a5cba1143f
author computational-metabolomics
date Thu, 13 Jun 2024 11:35:07 +0000
parents a0ee43397d1e
children
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5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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1 library(optparse)
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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2 library(msPurity)
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3 library(xcms)
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4 print(sessionInfo())
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7 get_av_spectra <- function(x) {
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8 if (length(x$av_intra) > 0) {
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9 av_intra_df <- plyr::ldply(x$av_intra)
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11 if (nrow(av_intra_df) == 0) {
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12 av_intra_df <- NULL
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13 } else {
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14 av_intra_df$method <- "intra"
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15 }
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16 } else {
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17 av_intra_df <- NULL
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18 }
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20 if ((is.null(x$av_inter)) || (nrow(x$av_inter) == 0)) {
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21 av_inter_df <- NULL
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22 } else {
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23 av_inter_df <- x$av_inter
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24 av_inter_df$method <- "inter"
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25 }
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27 if ((is.null(x$av_all)) || (nrow(x$av_all) == 0)) {
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28 av_all_df <- NULL
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29 } else {
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30 av_all_df <- x$av_all
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31 av_all_df$method <- "all"
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32 }
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34 combined <- plyr::rbind.fill(av_intra_df, av_inter_df, av_all_df)
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36 return(combined)
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37 }
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40 option_list <- list(
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41 make_option("--out_rdata", type = "character"),
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42 make_option("--out_peaklist", type = "character"),
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43 make_option("--pa", type = "character"),
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44 make_option("--av_level", type = "character"),
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45 make_option("--minfrac", default = 0.5),
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46 make_option("--minnum", default = 1),
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47 make_option("--ppm", default = 5.0),
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48 make_option("--snr", default = 0),
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49 make_option("--ra", default = 0),
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50 make_option("--av", default = "median", type = "character"),
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51 make_option("--sumi", action = "store_true"),
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52 make_option("--rmp", action = "store_true"),
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53 make_option("--cores", default = 1)
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54 )
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56 opt <- parse_args(OptionParser(option_list = option_list))
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57 print(opt)
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60 load_r_data <- function(rdata_path, name) {
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61 # loads an RData file, and returns the named xset object if it is there
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62 load(rdata_path)
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63 return(get(ls()[ls() %in% name]))
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64 }
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66 # Requires
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67 pa <- load_r_data(opt$pa, "pa")
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69 pa@cores <- opt$cores
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71 if (is.null(opt$rmp)) {
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72 rmp <- FALSE
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73 } else {
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74 rmp <- TRUE
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75 }
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77 if (is.null(opt$sumi)) {
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78 sumi <- FALSE
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79 } else {
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80 sumi <- TRUE
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81 }
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82
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83 if (opt$av_level == "intra") {
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84 pa <- msPurity::averageIntraFragSpectra(pa,
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85 minfrac = opt$minfrac,
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86 minnum = opt$minnum,
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87 ppm = opt$ppm,
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88 snr = opt$snr,
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89 ra = opt$ra,
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90 av = opt$av,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
91 sumi = sumi,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
92 rmp = rmp,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 6
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93 cores = opt$cores
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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94 )
6
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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95 } else if (opt$av_level == "inter") {
0
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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96 pa <- msPurity::averageInterFragSpectra(pa,
8
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
97 minfrac = opt$minfrac,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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98 minnum = opt$minnum,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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99 ppm = opt$ppm,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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100 snr = opt$snr,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
101 ra = opt$ra,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
102 av = opt$av,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
103 sumi = sumi,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 6
diff changeset
104 rmp = rmp,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
105 cores = opt$cores
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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106 )
6
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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107 } else if (opt$av_level == "all") {
0
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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108 pa <- msPurity::averageAllFragSpectra(pa,
8
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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109 minfrac = opt$minfrac,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
110 minnum = opt$minnum,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
111 ppm = opt$ppm,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 6
diff changeset
112 snr = opt$snr,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 6
diff changeset
113 ra = opt$ra,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
114 av = opt$av,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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115 sumi = sumi,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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116 rmp = rmp,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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117 cores = opt$cores
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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118 )
0
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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119 }
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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120
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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121 print(pa)
6
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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122 save(pa, file = opt$out_rdata)
0
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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123
6
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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124 if (length(pa) > 0) {
0
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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125 av_spectra <- plyr::ldply(pa@av_spectra, get_av_spectra)
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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126
6
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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127 if (nrow(av_spectra) == 0) {
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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128 message("No average spectra available")
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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129 } else {
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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130 colnames(av_spectra)[1] <- "grpid"
0
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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131 av_spectra$grpid <- names(pa@av_spectra)[av_spectra$grpid]
6
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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132
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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133 if ((length(pa@av_intra_params) > 0) || (length(pa@av_inter_params) > 0)) {
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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134 # Add some extra info (only required if av_intra or av_inter performed)
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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135 colnames(av_spectra)[2] <- "fileid"
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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136 av_spectra$avid <- seq_len(nrow(av_spectra))
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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137
8
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
138 filenames <- sapply(
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
139 av_spectra$fileid,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
140 function(x) names(pa@fileList)[as.integer(x)]
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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141 )
6
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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142 # filenames_galaxy <- sapply(
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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143 # av_spectra$fileid, function(x) basename(pa@fileList[as.integer(x)]))
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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144
8
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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diff changeset
145 av_spectra <- as.data.frame(
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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146 append(av_spectra, list(filename = filenames), after = 2)
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
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147 )
0
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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148 }
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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149
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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150
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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151 print(head(av_spectra))
6
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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152 write.table(av_spectra, opt$out_peaklist, row.names = FALSE, sep = "\t")
0
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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153 }
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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154 }