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6
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1 Wrappers for:
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2 - the metaMS R package by Ron Wehrens.
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3 - the xcms package.
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4
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5 Wrappers written by Pieter Lukasse.
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6
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7
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8 Installation (when updating: close all vignettes [i.e. pdfs/manuals] !)
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9
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10 In R:
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11 source("http://bioconductor.org/biocLite.R")
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12 biocLite("metaMS")
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13 biocLite("multtest")
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14 #biocLite("R2HTML")
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15 # for "multi-threading" (actually starts multiple R processes for parallel processing):
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16 install.packages("snow")
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17 install.packages("Cairo")
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18
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19 ======Run metaMS_cmd_pick_and_group.r with:=================
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20
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21 E:\workspace\PRIMS-metabolomics\python-tools\tools\metaMS>Rscript metaMS_cmd_pick_and_group.r test/extdata.zip test/example_settings.txt test/out/peakTable.txt test/out/xsAnnotatePrep.rdata positive test/out/html_peaks.html test/out
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22
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23
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24 ======Run metaMS_cmd_annotate.r with:=================
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25
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26 E:\workspace\PRIMS-metabolomics\python-tools\tools\metaMS>Rscript metaMS_cmd_annotate.r test/LCDBtest.RData test/out/xsAnnotatePrep.rdata test/example_settings.txt test/out/annotationTable.txt "0" test/out/html_annot.html test/out
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27
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28
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29 ======Run xcms_differential_analysis.r with:=================
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30
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31 E:\workspace\PRIMS-metabolomics\python-tools\tools\metaMS>Rscript xcms_differential_analysis.r test/out/xsAnnotatePrep.rdata "CLASS1" "CLASS2" 10 test/out2/outtable.tsv test/out2/html/html.html test/out2/html
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32
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33
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34 ======Run xcms_get_eic.r with:=================
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35
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36
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37 E:\workspace\PRIMS-metabolomics\python-tools\tools\metaMS>Rscript xcms_get_alignment_eic.r test/out/xsAnnotatePrep.rdata 10 300 3 STDmix_GC_01,STDmix_GC_02 test/out3/html/html.html test/out3/html
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38
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39 OR
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40
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41 E:\workspace\PRIMS-metabolomics\python-tools\tools\metaMS>Rscript xcms_get_mass_eic.r test/out/xsAnnotatePrep.rdata 10 3000 -1 -1 "77.98,231.96" 5 STDmix_GC_01,STDmix_GC_02 Yes raw test/out4/html/html.html test/out4/html
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42
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43
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44
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45 !!!!!!!!!!!!!!!!Troubleshooting:!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
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46
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47
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48 NetCDF is required. If the following is found in the installation.log
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49
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50 In file included from rnetCDF.c:2:0:
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51 rnetCDF.h:1:20: fatal error: netcdf.h: No such file or directory
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52 compilation terminated.
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53
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54
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55 then metaMS will not have been installed and running the tool will result in error:
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56 <simpleError in library(metaMS): there is no package called 'metaMS'>
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57
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58 Possible solution:
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59 > Install the -dev of those packages to get the headers that are
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60 required to compile the package. In this case, you need libnetcdf-dev, udunits-bin and libudunits2-dev
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61 (from http://stackoverflow.com/questions/11319698/how-to-install-r-packages-rnetcdf-and-ncdf-on-ubuntu)
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62 So
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63 >>sudo apt-get install libnetcdf-dev, udunits-bin and libudunits2-dev
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64
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65 Cairo / no X11 mode is required.
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66
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67 Possible solution:
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68 > install of cairo (http://www.cairographics.org/) and/or set CAIRO_CFLAGS/LIBS correspondingly.
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69 So
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70 >>sudo apt-get install libcairo2-dev
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