Hi,

I'm currently using the new xcms function which executes the following command

raw_data <- readMSData(files = cdfs, pdata = new("NAnnotatedDataFrame", pd), mode = "onDisk") 

The command uses OnDiskMSnExp object from MSnbase Bioconductor package. May i know if i made any changes such as retention time alignment using the following command

xdata <- adjustRtime(xdata, param = ObiwarpParam(binSize = 0.6)) 

Does it overwrites my original files ? or it juz creates a new data in Rstudio environment?

Thank you.

Goh. 

Hi Goh,

No, your original data isn't modified at all. The only way to modify raw data on disk is to write it explicitly to a file using writeMSData. Note however that in your example, the raw data object raw_data, once created, isn't modified at all, as you use xdata to adjust retention time - probably only a result of copy/pasting parts of a longer script.