Mercurial > repos > marie-tremblay-metatoul > normalization

annotate NmrNormalization_script.R @ 3:966fcf7ae66e draft

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planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
author lecorguille
date Thu, 26 Oct 2017 06:01:14 -0400
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children 221cbd549c40
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966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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1 #################################################################################################################
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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2 # SPECTRA NORMALIZATION FROM SPECTRAL DATA #
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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3 # User : Galaxy #
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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4 # Original data : -- #
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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5 # Starting date : 20-10-2014 #
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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6 # Version 1 : 27-01-2015 #
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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7 # Version 2 : 27-02-2015 #
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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8 # #
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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9 # Input files: #
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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10 # - Data matrix containing bucketed and integrated spectra to normalize #
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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11 # - Sample metadata matrix containing at least biological factor of interest #
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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12 # - Scaling method: Total intensity/Probabilistic Quotient Normalization #
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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13 # - Control group: name of control to compute median reference spectra #
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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14 # - Graph: normalization result representation #
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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15 #################################################################################################################
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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16 NmrNormalization <- function(dataMatrix,scalingMethod=c("None","Total","PQN","BioFactor"),sampleMetadata=NULL,
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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17 bioFactor=NULL,ControlGroup=NULL,graph=c("None","Overlay","One_per_individual"),
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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18 nomFichier=NULL,savLog.txtC=NULL)
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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19 {
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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21 ## Option
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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22 ##---------------
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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23 strAsFacL <- options()$stringsAsFactors
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24 options(stingsAsFactors = FALSE)
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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25 options(warn = -1)
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966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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28 ## Constants
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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29 ##---------------
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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30 topEnvC <- environment()
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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31 flgC <- "\n"
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32
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33 ## Log file (in case of integration into Galaxy)
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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34 ##----------------------------------------------
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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35 if(!is.null(savLog.txtC))
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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36 sink(savLog.txtC, append = TRUE)
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38 ## Functions definition
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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39 ##---------------------
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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40 #################################################################################################################
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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41 # Total intensity normalization
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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42 # Input parameters
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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43 # - data : bucketed spectra (rows=buckets; columns=samples)
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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44 #################################################################################################################
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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45 NmrBrucker_total <- function(data)
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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46 {
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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47 # Total intensity normalization
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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48 data.total <- apply(data,2,sum)
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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49 data.normalized <- data[,1]/data.total[1]
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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50 for (i in 2:ncol(data))
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51 data.normalized <- cbind(data.normalized,data[,i]/data.total[i])
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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52 colnames(data.normalized) <- colnames(data)
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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53 rownames(data.normalized) <- rownames(data)
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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54 return(data.normalized)
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55 }
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56
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57
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58 #################################################################################################################
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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59 # Biological factor normalization
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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60 # Input parameters
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61 # - data : bucketed spectra (rows=buckets; columns=samples)
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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62 # - sampleMetadata : dataframe with biological factor of interest measured for each invidual
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63 # - bioFactor : name of the column cotaining the biological factor of interest
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64 #################################################################################################################
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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65 NmrBrucker_bioFact <- function(data,sampleMetadata,bioFactor)
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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66 {
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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67 # Total intensity normalization
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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68 data.normalized <- data[,1]/bioFactor[1]
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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69 for (i in 2:ncol(data))
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70 data.normalized <- cbind(data.normalized,data[,i]/bioFactor[i])
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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71 colnames(data.normalized) <- colnames(data)
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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72 rownames(data.normalized) <- rownames(data)
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73 return(data.normalized)
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74 }
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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75
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76
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77 #################################################################################################################
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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78 # Probabilistic quotient normalization (PQN)
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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79 # Input parameters
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80 # - data : bucketed spectra (rows=buckets; columns=samples)
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81 # - sampleMetadata : dataframe with treatment group of inviduals
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82 # - pqnFactor : number of the column cotaining the biological facor of interest
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83 # - nomControl : name of the treatment group
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84 #################################################################################################################
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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85 NmrBrucker_pqn <- function(data,sampleMetadata,pqnFactor,nomControl)
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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86 {
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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87 # Total intensity normalization
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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88 data.total <- apply(data,2,sum)
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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89 data.normalized <- data[,1]/data.total[1]
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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90 for (i in 2:ncol(data))
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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91 data.normalized <- cbind(data.normalized,data[,i]/data.total[i])
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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92 colnames(data.normalized) <- colnames(data)
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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93 rownames(data.normalized) <- rownames(data)
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94
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95 # Reference spectrum
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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96 # Recuperation spectres individus controle
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97 control.spectra <- data.normalized[,sampleMetadata[,pqnFactor]==nomControl]
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98 spectrum.ref <- apply(control.spectra,1,median)
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99
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100 # Ratio between normalized and reference spectra
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101 data.normalized.ref <- data.normalized/spectrum.ref
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102
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103 # Median ratio
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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104 data.normalized.ref.median <- apply(data.normalized.ref,1,median)
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105
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106 # Normalization
966fcf7ae66e planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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107 data.normalizedPQN <- data.normalized[,1]/data.normalized.ref.median
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108 for (i in 2:ncol(data))
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109 data.normalizedPQN <- cbind(data.normalizedPQN,data.normalized[,i]/data.normalized.ref.median)
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110 colnames(data.normalizedPQN) <- colnames(data)
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111 rownames(data.normalizedPQN) <- rownames(data)
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112
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113 return(data.normalizedPQN)
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114 }
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115
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116
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117 ## Tests
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118 if (scalingMethod=="QuantitativeVariable")
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119 {
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120 if(mode(sampleMetadata[,bioFactor]) == "character")
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121 bioFact <- factor(sampleMetadata[,bioFactor])
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122 else
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123 bioFact <- sampleMetadata[,bioFactor]
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124 }
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125
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126 ## Spectra scaling depending on the user choice
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127 if (scalingMethod == "None")
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128 {
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129 NormalizedBucketedSpectra <- dataMatrix
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130 }
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131 else if (scalingMethod == "Total")
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132 {
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133 NormalizedBucketedSpectra <- NmrBrucker_total(dataMatrix)
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134 }
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135 else if (scalingMethod == "PQN")
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136 {
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137 NormalizedBucketedSpectra <- NmrBrucker_pqn(dataMatrix,sampleMetadata,bioFactor,ControlGroup)
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138 }
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139 else if (scalingMethod == "QuantitativeVariable")
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140 {
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141 NormalizedBucketedSpectra <- NmrBrucker_bioFact(dataMatrix,sampleMetadata,bioFact)
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142 }
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143
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144 ## OUTPUTS
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145 return(list(NormalizedBucketedSpectra))
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146
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147 }