Raw MS data processing using xcms.
processData( path = ".", polarity = c("positive", "negative"), ppm = 15, peakwidth = c(5, 30), snthresh = 10, prefilter = c(3, 500), fitgauss = FALSE, integrate = 2, mzdiff = 0.01, noise = 500, threads = 6, binSize = 0.025, bw = 5, output.tic = TRUE, output.bpc = TRUE, output.rt.correction.plot = TRUE, min.fraction = 0.5, fill.peaks = FALSE, output.peak.eic = TRUE, is.table = "is.table.xlsx", is.mz.tolerance = 25, is.rt.tolerance = 50, group.for.figure = "QC" )
| path | Work directory. |
|---|---|
| polarity | The polarity of data, "positive"or "negative". |
| ppm | see xcms. |
| peakwidth | See xcms. |
| snthresh | See xcms. |
| prefilter | See xcms. |
| fitgauss | see xcms. |
| integrate | see xcms. |
| mzdiff | see xcms. |
| noise | See xcms. |
| threads | Number of threads. |
| binSize | see xcms. |
| bw | see xcms. |
| output.tic | Output TIC plot or not. |
| output.bpc | Output BPC plot or not. |
| output.rt.correction.plot | Output rt correction plot or not. |
| min.fraction | See xcms. |
| fill.peaks | Fill peaks NA or not. |
| output.peak.eic | Output some peaks EIC or not. If you want to output this, please place the 'is.xlsx' in the folder. And three columns, name, mz and rt. |
| is.table | International standard table name. |
| is.mz.tolerance | mz tolerance for internal standards. Default is 25 ppm. |
| is.rt.tolerance | RT tolerance for internal standards. Default is 50 s.. |
| group.for.figure | Which group you want to use to output TIC and BPC and EIC. Default is QC. |
Peak table.
Xiaotao Shen shenxt1990@163.com