Mercurial > repos > marie-tremblay-metatoul > normalization
annotate NmrNormalization_script.R @ 3:966fcf7ae66e draft
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
author | lecorguille |
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date | Thu, 26 Oct 2017 06:01:14 -0400 |
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children | 221cbd549c40 |
rev | line source |
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3
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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1 ################################################################################################################# |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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2 # SPECTRA NORMALIZATION FROM SPECTRAL DATA # |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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3 # User : Galaxy # |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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changeset
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4 # Original data : -- # |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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changeset
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5 # Starting date : 20-10-2014 # |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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changeset
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6 # Version 1 : 27-01-2015 # |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
diff
changeset
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7 # Version 2 : 27-02-2015 # |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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changeset
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8 # # |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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changeset
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9 # Input files: # |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
diff
changeset
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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
lecorguille
parents:
diff
changeset
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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
lecorguille
parents:
diff
changeset
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12 # - Scaling method: Total intensity/Probabilistic Quotient Normalization # |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
diff
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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
lecorguille
parents:
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changeset
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14 # - Graph: normalization result representation # |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
diff
changeset
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15 ################################################################################################################# |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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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
lecorguille
parents:
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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
lecorguille
parents:
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18 nomFichier=NULL,savLog.txtC=NULL) |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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19 { |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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20 |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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21 ## Option |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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22 ##--------------- |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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23 strAsFacL <- options()$stringsAsFactors |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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24 options(stingsAsFactors = FALSE) |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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changeset
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25 options(warn = -1) |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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26 |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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27 |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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28 ## Constants |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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29 ##--------------- |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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30 topEnvC <- environment() |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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31 flgC <- "\n" |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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changeset
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32 |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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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
lecorguille
parents:
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34 ##---------------------------------------------- |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
diff
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35 if(!is.null(savLog.txtC)) |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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36 sink(savLog.txtC, append = TRUE) |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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37 |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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38 ## Functions definition |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
diff
changeset
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39 ##--------------------- |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
diff
changeset
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40 ################################################################################################################# |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
diff
changeset
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41 # Total intensity normalization |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
diff
changeset
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42 # Input parameters |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
diff
changeset
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43 # - data : bucketed spectra (rows=buckets; columns=samples) |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
diff
changeset
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44 ################################################################################################################# |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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45 NmrBrucker_total <- function(data) |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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46 { |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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47 # Total intensity normalization |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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48 data.total <- apply(data,2,sum) |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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49 data.normalized <- data[,1]/data.total[1] |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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50 for (i in 2:ncol(data)) |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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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
lecorguille
parents:
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52 colnames(data.normalized) <- colnames(data) |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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53 rownames(data.normalized) <- rownames(data) |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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54 return(data.normalized) |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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55 } |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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56 |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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57 |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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58 ################################################################################################################# |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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59 # Biological factor normalization |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
diff
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60 # Input parameters |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
diff
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61 # - data : bucketed spectra (rows=buckets; columns=samples) |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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62 # - sampleMetadata : dataframe with biological factor of interest measured for each invidual |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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63 # - bioFactor : name of the column cotaining the biological factor of interest |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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64 ################################################################################################################# |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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65 NmrBrucker_bioFact <- function(data,sampleMetadata,bioFactor) |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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66 { |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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67 # Total intensity normalization |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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68 data.normalized <- data[,1]/bioFactor[1] |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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69 for (i in 2:ncol(data)) |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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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
lecorguille
parents:
diff
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71 colnames(data.normalized) <- colnames(data) |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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72 rownames(data.normalized) <- rownames(data) |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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73 return(data.normalized) |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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74 } |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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75 |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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76 |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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77 ################################################################################################################# |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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78 # Probabilistic quotient normalization (PQN) |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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79 # Input parameters |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
diff
changeset
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80 # - data : bucketed spectra (rows=buckets; columns=samples) |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
diff
changeset
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81 # - sampleMetadata : dataframe with treatment group of inviduals |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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82 # - pqnFactor : number of the column cotaining the biological facor of interest |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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83 # - nomControl : name of the treatment group |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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84 ################################################################################################################# |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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85 NmrBrucker_pqn <- function(data,sampleMetadata,pqnFactor,nomControl) |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
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86 { |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
diff
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87 # Total intensity normalization |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
lecorguille
parents:
diff
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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] |
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planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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90 for (i in 2:ncol(data)) |
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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]) |
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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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planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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94 |
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planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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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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planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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97 control.spectra <- data.normalized[,sampleMetadata[,pqnFactor]==nomControl] |
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planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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98 spectrum.ref <- apply(control.spectra,1,median) |
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planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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99 |
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planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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100 # Ratio between normalized and reference spectra |
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planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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101 data.normalized.ref <- data.normalized/spectrum.ref |
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planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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102 |
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planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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103 # Median ratio |
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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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planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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105 |
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106 # Normalization |
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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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planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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108 for (i in 2:ncol(data)) |
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planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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109 data.normalizedPQN <- cbind(data.normalizedPQN,data.normalized[,i]/data.normalized.ref.median) |
966fcf7ae66e
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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110 colnames(data.normalizedPQN) <- colnames(data) |
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planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
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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 } |