Mercurial > repos > dlalgroup > pmids_to_pubtator_matrix

annotate pmids_to_pubtator_matrix.R @ 2:ada4c7b3fc39 draft default tip

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"planemo upload for repository https://github.com/dlal-group/simtext commit 63f67ee02be2eb4323a5ba5dcdd33d1fd0b7c24e"
author dlalgroup
date Thu, 08 Oct 2020 05:39:58 +0000
parents 3f4adc85ba5d
children
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1 #!/usr/bin/env Rscript
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2 #tool: pmids_to_pubtator_matrix
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3 #
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4 #The tool uses all PMIDs per row and extracts "Gene", "Disease", "Mutation", "Chemical" and "Species" terms of the
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5 #corresponding abstracts, using PubTator annotations. The user can choose from which categories terms should be extracted.
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6 #The extracted terms are united in one large binary matrix, with 0= term not present in abstracts of that row and 1= term
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7 #present in abstracts of that row. The user can decide if the extracted scientific terms should be extracted and used as
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8 #they are or if they should be grouped by their geneIDs/ meshIDs (several terms can often be grouped into one ID).
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9 #äAlso, by default all terms are extracted, otherwise the user can specify a number of most frequent words to be extracted per row.
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10 #
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11 #Input: Output of abstracts_by_pmids or tab-delimited table with columns containing PMIDs.
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12 #The names of the PMID columns should start with "PMID", e.g. "PMID_1", "PMID_2" etc.
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13 #
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14 #Output: Binary matrix in that each column represents one of the extracted terms.
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15 #
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16 # usage: $ pmids_to_pubtator_matrix.R [-h] [-i INPUT] [-o OUTPUT] [-n NUMBER]
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17 # [-c {Genes,Diseases,Mutations,Chemicals,Species} [{Genes,Diseases,Mutations,Chemicals,Species} ...]]
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18 #
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19 # optional arguments:
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20 # -h, --help show help message
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21 # -i INPUT, --input INPUT input file name. add path if file is not in workind directory
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22 # -n NUMBER, --number NUMBER Number of most frequent terms/IDs to extract. By default all terms/IDs are extracted.
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23 # -o OUTPUT, --output OUTPUT output file name. [default "pmids_to_pubtator_matrix_output"]
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24 # -c {Gene,Disease,Mutation,Chemical,Species} [{Genes,Diseases,Mutations,Chemicals,Species} ...], --categories {Gene,Disease,Mutation,Chemical,Species} [{Gene,Disease,Mutation,Chemical,Species} ...]
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25 # Pubtator categories that should be considered. [default "('Gene', 'Disease', 'Mutation','Chemical')"]
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26
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27 if ( '--install_packages' %in% commandArgs()) {
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28 print('Installing packages')
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29 if (!require('argparse')) install.packages('argparse',repo="http://cran.rstudio.com/");
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30 if (!require('stringr')) install.packages('stringr',repo="http://cran.rstudio.com/");
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31 if (!require('RCurl')) install.packages('RCurl',repo="http://cran.rstudio.com/");
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32 if (!require('stringi')) install.packages('stringi',repo="http://cran.rstudio.com/");
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33 }
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34
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35 suppressPackageStartupMessages(library("argparse"))
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36 library('stringr')
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37 library('stringi')
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38 library('RCurl')
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39
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40 parser <- ArgumentParser()
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41
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42 parser$add_argument("-i", "--input",
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43 help = "input fie name. add path if file is not in workind directory")
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44 parser$add_argument("-o", "--output", default="pmids_to_pubtator_matrix_output",
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45 help = "output file name. [default \"%(default)s\"]")
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46 parser$add_argument("-c", "--categories", choices=c("Gene", "Disease", "Mutation", "Chemical", "Species"), nargs="+",
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47 default= c("Gene", "Disease", "Mutation", "Chemical"),
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48 help = "Pubtator categories that should be considered. [default \"%(default)s\"]")
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49 parser$add_argument("-b", "--byid", action="store_true", default=FALSE,
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50 help="If you want to find common gene IDs / mesh IDs instead of scientific terms.")
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51 parser$add_argument("-n", "--number", default=NULL, type="integer",
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52 help="Number of most frequent terms/IDs to extract. By default all terms/IDs are extracted.")
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53 parser$add_argument("--install_packages", action="store_true", default=FALSE,
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54 help="If you want to auto install missing required packages.")
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55
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56 args <- parser$parse_args()
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57
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58
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59 data = read.delim(args$input, stringsAsFactors=FALSE, header = TRUE, sep='\t')
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60
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61 pmid_cols_index <- grep(c("PMID"), names(data))
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62 word_matrix = data.frame()
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63 dict.table = data.frame()
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64 pmids_count <- 0
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65 pubtator_max_ids = 100
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66
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67 get_pubtator_terms = function(pmids, categories){
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68
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69 table = NULL
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70 for (pmid_split in split(pmids, ceiling(seq_along(pmids)/pubtator_max_ids))){
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71 out.data = NULL
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72 try_num <- 1
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73 t_0 <- Sys.time()
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74
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75 while(TRUE) {
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76
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77 # Timing check: kill at 3 min
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78 if (try_num > 1){
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79 cat("Connection problem. Please wait. Try number:",try_num,"\n")
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80 Sys.sleep(time = 2*try_num)
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81 }
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82 try_num <- try_num + 1
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83
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84 t_1 <- Sys.time()
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85
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86 if(as.numeric(difftime(t_1, t_0, units = "mins")) > 3){
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87 message("Killing the request! Something is not working. Please, try again later","\n")
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
88 return(table)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
89 }
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
90 out.data <- tryCatch({
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
91 getURL(paste("https://www.ncbi.nlm.nih.gov/research/pubtator-api/publications/export/pubtator?pmids=",
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
92 paste(pmid_split, collapse=","), sep = ""))
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
93 }, error = function(e) {
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
94 print(e)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
95 next
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
96 }, finally = {
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
97 Sys.sleep(0)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
98 })
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
99
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
100 if(!is.null(out.data)){
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
101 out.data = unlist(strsplit(out.data, "\n", fixed = T))
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
102
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
103 # skip first few lines, is this needed?
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
104 for (i in 3:length(out.data)) {
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
105 temps = unlist(strsplit(out.data[i], "\t", fixed = T))
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
106 if (length(temps) == 5) {
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
107 # make 5 be 6
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
108 temps = c(temps, NA)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
109 }
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
110 if (length(temps) == 6) {
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
111 # keep only 6
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
112 table = rbind(table, temps)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
113 }
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
114 }
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
115 break
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
116 }
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
117
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
118 } #end while loop
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
119 }
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
120
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
121 index.categories = c()
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
122 categories = as.character(unlist(categories))
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
123
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
124 if(ncol(table) == 6){
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
125
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
126 for(i in categories){
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
127 tmp.index = grep(TRUE, i == as.character(table[,5]))
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
128
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
129 if(length(tmp.index) > 0){
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
130 index.categories = c(index.categories,tmp.index)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
131 }
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
132 }
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
133
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
134 table = as.data.frame(table, stringsAsFactors=FALSE)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
135 table = table[index.categories,c(4,6)]
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
136 table = table[!is.na(table[,2]),]
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
137 table = table[!(table[,2] == "NA"),]
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
138 table = table[!(table[,1] == "NA"),]
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
139
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
140 if(args$byid){
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
141 if(!is.null(args$number)){
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
142 #retrieve top X mesh.ids
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
143 table.mesh = as.data.frame(table(table[,2]))
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
144 colnames(table.mesh)[1] = "mesh.id"
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
145 table = table[order(table.mesh$Freq, decreasing = TRUE),]
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
146 table = table[1:min(args$number, nrow(table.mesh)),]
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
147 table.mesh$mesh.id = as.character(table.mesh$mesh.id)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
148 #subset table for top X mesh.ids
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
149 table = table[which(as.character(table$V6) %in% as.character(table.mesh$mesh.id)),]
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
150 table = table[!duplicated(table[,2]),]
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
151 }else{
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
152 table = table[!duplicated(table[,2]),]
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
153 }
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
154 } else {
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
155 if(!is.null(args$number)){
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
156 table[,1] = tolower(as.character(table[,1]))
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
157 table = as.data.frame(table(table[,1]))
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
158 colnames(table)[1] = "term"
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
159 table = table[order(table$Freq, decreasing = TRUE),]
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
160 table = table[1:min(args$number, nrow(table)),]
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
161 table$term = as.character(table$term)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
162
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
163 }else{
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
164 table[,1] = tolower(as.character(table[,1]))
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
165 table = table[!duplicated(table[,1]),]
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
166 }
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
167 }
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
168
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
169 return(table)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
170
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
171 } else {
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
172 return(NULL)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
173 }
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
174 }
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
175
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
176
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
177 #for all PMIDs of a row get PubTator terms and add them to the matrix
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
178 for (i in 1:nrow(data)){
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
179
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
180 pmids = as.character(data[i,pmid_cols_index])
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
181 pmids = pmids[!pmids == "NA"]
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182
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183
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parents:
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184 if ( (pmids_count > 10000)){
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dlalgroup
parents:
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185 cat("Break (10s) to avoid killing of requests. Please wait.",'\n')
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
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186 Sys.sleep(10)
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dlalgroup
parents:
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187 pmids_count = 0
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parents:
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188 }
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parents:
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189
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dlalgroup
parents:
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190 pmids_count = pmids_count + length(pmids)
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parents:
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191
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dlalgroup
parents:
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192 #get puptator terms with get_pubtator_terms function
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dlalgroup
parents:
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193 if (length(pmids) >0){
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dlalgroup
parents:
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194 table = get_pubtator_terms(pmids, args$categories)
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195
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dlalgroup
parents:
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196 if(!is.null(table)){
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197
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dlalgroup
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198 colnames(table)= c("term","mesh.id")
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199
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parents:
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200 # add data in binary matrix
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dlalgroup
parents:
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201 if (args$byid){
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dlalgroup
parents:
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202 mesh.ids = as.character(table$mesh.id)
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dlalgroup
parents:
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203 if (length(mesh.ids) > 0 ){
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dlalgroup
parents:
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204 word_matrix[i,mesh.ids] <- 1
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dlalgroup
parents:
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205 cat(length(mesh.ids), " IDs for PMIDs of row", i," were added",'\n')
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
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206 # add data in dictionary
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dlalgroup
parents:
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207 dict.table = rbind(dict.table, table)
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dlalgroup
parents:
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208 dict.table = dict.table[!duplicated(as.character(dict.table[,2])),]
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dlalgroup
parents:
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209 }
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dlalgroup
parents:
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210 } else {
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dlalgroup
parents:
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211 terms = as.character(table[,1])
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dlalgroup
parents:
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212 if (length(terms) > 0 ){
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dlalgroup
parents:
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213 word_matrix[i,terms] <- 1
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dlalgroup
parents:
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214 cat(length(terms), " terms for PMIDs of row", i," were added.",'\n')
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dlalgroup
parents:
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215 }
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dlalgroup
parents:
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216 }
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parents:
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217 }
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218
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parents:
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219 } else {
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dlalgroup
parents:
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220 cat("No terms for PMIDs of row", i," were found.",'\n')
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dlalgroup
parents:
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221 }
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dlalgroup
parents:
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222 }
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223
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parents:
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224 if (args$byid){
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dlalgroup
parents:
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225 #change column names of matrix: exchange mesh ids/ids with term
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dlalgroup
parents:
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226 index_names = match(names(word_matrix), as.character(dict.table[[2]]))
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dlalgroup
parents:
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227 names(word_matrix) = dict.table[index_names,1]
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dlalgroup
parents:
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228 }
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229
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dlalgroup
parents:
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230 colnames(word_matrix) = gsub("[^[:print:]]","",colnames(word_matrix))
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dlalgroup
parents:
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231 colnames(word_matrix) = gsub('\"', "", colnames(word_matrix), fixed = TRUE)
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232
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dlalgroup
parents:
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233 #merge duplicated columns
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dlalgroup
parents:
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234 word_matrix = as.data.frame(do.call(cbind, by(t(word_matrix),INDICES=names(word_matrix),FUN=colSums)))
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dlalgroup
parents:
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235
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dlalgroup
parents:
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236 #save binary matrix
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dlalgroup
parents:
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237 word_matrix <- as.matrix(word_matrix)
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dlalgroup
parents:
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238 word_matrix[is.na(word_matrix)] <- 0
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dlalgroup
parents:
diff changeset
239 cat("Matrix with ",nrow(word_matrix)," rows and ",ncol(word_matrix)," columns generated.","\n")
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dlalgroup
parents:
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240 #write.table(word_matrix, args$output)
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dlalgroup
parents:
diff changeset
241 write.table(word_matrix, args$output, row.names = FALSE, sep = '\t')
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242
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243
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247