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CAMERA / slot neutraladdition can not be empty to use generateRules
> 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
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> 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
>