I try the following:
> rsP <- new("ruleSet")
> rsP@ionlistfile <- "ions_pos.csv"
> rsP@neutraladditionfile <- "neutraladdition.csv"
> rsP@neutrallossfile <- "neutralloss.csv"
> rsP <- readLists(rsP)
> rsP <- setDefaultParams(rsP)
> rsP <- generateRules(rsP)
Fehler in if (neutraladdition[i, 1] == "NaCOOH") { :
Fehlender Wert, wo TRUE/FALSE nötig ist
which is because neutraladdition.csv just has the header and no entries which creates an empty slot of neutraladdition. I do not want to allow a neutral addition in my rule set. Is there a possibility to fix that? I guess the problem is in the section "## Erzeuge Neutral" of ruleSet.R
Many Thanks,
Andre
------
> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 LC_MONETARY=German_Germany.1252
[4] LC_NUMERIC=C LC_TIME=German_Germany.1252
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] ProbMetab_1.0 rjson_0.2.14 multtest_2.20.0 XML_3.98-1.1
[5] RCurl_1.95-4.3 bitops_1.0-6 hwriter_1.3.2 RCytoscape_1.14.0
[9] XMLRPC_0.3-0 graph_1.42.0 GeneNet_1.2.10 fdrtool_1.2.12
[13] longitudinal_1.1.9 corpcor_1.6.6 RcppArmadillo_0.4.400.0 CAMERA_1.20.0
[17] igraph_0.7.1 xcms_1.40.0 Biobase_2.24.0 BiocGenerics_0.10.0
[21] mzR_1.10.7 Rcpp_0.11.2
loaded via a namespace (and not attached):
[1] acepack_1.3-3.3 cluster_1.15.3 codetools_0.2-9 foreign_0.8-61 Formula_1.1-2
[6] grid_3.1.0 Hmisc_3.14-5 lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-34
[11] nnet_7.3-8 RBGL_1.40.1 RColorBrewer_1.0-5 rpart_4.1-8 splines_3.1.0
[16] stats4_3.1.0 survival_2.37-7 tools_3.1.0
>
Hi Andre,
Thanks for reporting this, I am tracking this now at https://github.com/sneumann/CAMERA/issues/5 (https://github.com/sneumann/CAMERA/issues/5)
Yours,
Steffen
Hi Andre,
can you check the branch at https://github.com/sneumann/CAMERA/tree ... erateRules (https://github.com/sneumann/CAMERA/tree/fixGenerateRules) ?
Yours,
Steffen
Hi Andre,
did the fix work for you ?
Yours,
Steffen
Hi Steffen,
Sorry it took me two days to get github devtools in R running on Windows. Finally it works in R on cmd shell but not in the windows R console.... Do not ask me why...
Yes it works:
> rsP@rules
name nmol charge massdiff oidscore quasi ips
1 [M+H]+ 1 1 1.007276 1 1 1.00
5 [M+Na]+ 1 1 22.989218 5 1 1.00
6 [M+2Na-H]+ 1 1 44.971160 6 0 0.25
7 [M+H-H20]+ 1 1 -17.008024 7 0 0.25
Well I guess 6 is very very unlikely. Is there a parameter that can omit ion 6? Or should I directly delete it with rsP@rules[c(1,2,4),]->rsP@rules
Thanks for your help,
Andre
6 is not that unlikely at all. It is
relatively common at least in some instruments. Plot from my thesis (http://https://www.researchgate.net/publication/262009547_Metabolomics_investigation_of_whey_intake_Discovery_of_markers_and_biological_effects_supported_by_a_computer-assisted_compound_identification_pipeline):
[attachment=0:12m8jyhl]adducts_combined2.png[/attachment:12m8jyhl]
You can get the rules I used (http://https://github.com/stanstrup/chemhelper/tree/master/inst/extdata) or load them with load.camera.rules from my package (http://https://github.com/stanstrup/chemhelper) if they would be useful to you.
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Hi Andre,
I pushed the change to the devel branch, should appear in a few days.
Package: CAMERA
Version: 1.23.1
Date: 2014-11-16
Yours,
Steffen