Mercurial > repos > lecorguille > xcms_xcmsset

comparison xcms_xcmsSet.r @ 37:9ada611dd63f draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e
author lecorguille
date Fri, 31 Aug 2018 08:59:03 -0400
parents d39b9aff9cf7
children e8d7395a70b2
comparison
equal deleted inserted replaced
36:d39b9aff9cf7 37:9ada611dd63f
81 81
82 cat("\t\t\tApply filter[s] (if asked)\n") 82 cat("\t\t\tApply filter[s] (if asked)\n")
83 if (exists("filterAcquisitionNumParam")) raw_data <- filterAcquisitionNum(raw_data, filterAcquisitionNumParam[1]:filterAcquisitionNumParam[2]) 83 if (exists("filterAcquisitionNumParam")) raw_data <- filterAcquisitionNum(raw_data, filterAcquisitionNumParam[1]:filterAcquisitionNumParam[2])
84 if (exists("filterRtParam")) raw_data <- filterRt(raw_data, filterRtParam) 84 if (exists("filterRtParam")) raw_data <- filterRt(raw_data, filterRtParam)
85 if (exists("filterMzParam")) raw_data <- filterMz(raw_data, filterMzParam) 85 if (exists("filterMzParam")) raw_data <- filterMz(raw_data, filterMzParam)
86 #Apply this filter only if file contain MS and MSn
87 if(length(unique(msLevel(raw_data)))!= 1){
88 raw_data <- filterMsLevel(raw_data,msLevel=1)
89 }
86 90
87 cat("\t\t\tChromatographic peak detection\n") 91 cat("\t\t\tChromatographic peak detection\n")
88 # clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or method ... 92 # clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or method ...
89 args <- args[names(args) %in% slotNames(do.call(paste0(method,"Param"), list()))] 93 args <- args[names(args) %in% slotNames(do.call(paste0(method,"Param"), list()))]
90 94