Mercurial > repos > lecorguille > xcms_retcor
comparison xcms_retcor.r @ 46:32c1cbdbdd3b draft
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 665b0684ed3cd1db5d297e0265c59787f8b66289"
| author | workflow4metabolomics |
|---|---|
| date | Thu, 13 Feb 2020 11:42:41 +0000 |
| parents | 1986c48d86ce |
| children | 366ff564f949 |
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| 45:1986c48d86ce | 46:32c1cbdbdd3b |
|---|---|
| 61 # clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or method ... | 61 # clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or method ... |
| 62 args <- args[names(args) %in% slotNames(do.call(paste0(method,"Param"), list()))] | 62 args <- args[names(args) %in% slotNames(do.call(paste0(method,"Param"), list()))] |
| 63 | 63 |
| 64 adjustRtimeParam <- do.call(paste0(method,"Param"), args) | 64 adjustRtimeParam <- do.call(paste0(method,"Param"), args) |
| 65 print(adjustRtimeParam) | 65 print(adjustRtimeParam) |
| 66 | |
| 67 if (hasAdjustedRtime(xdata)) { | |
| 68 cat("WARNING: a retention time ajustment had already been applied to your data.\nThe function applyAdjustedRtime was processed to cumulate the ajustment") | |
| 69 cat("Replace raw retention times with adjusted retention times.\n") | |
| 70 xdata <- applyAdjustedRtime(xdata) | |
| 71 } | |
| 66 xdata <- adjustRtime(xdata, param=adjustRtimeParam) | 72 xdata <- adjustRtime(xdata, param=adjustRtimeParam) |
| 67 | 73 |
| 68 #cat("\t\t\tCompute and Store TIC and BPI\n") | 74 #cat("\t\t\tCompute and Store TIC and BPI\n") |
| 69 #chromTIC_adjusted = chromatogram(xdata, aggregationFun = "sum") | 75 #chromTIC_adjusted = chromatogram(xdata, aggregationFun = "sum") |
| 70 #chromBPI_adjusted = chromatogram(xdata, aggregationFun = "max") | 76 #chromBPI_adjusted = chromatogram(xdata, aggregationFun = "max") |