I would like to filter my data by R. However, I am very new in R.
Subtracting the blank spectrum
Filtering samples by QC
Subtracting the m/z lower than 3000.
Is there any good packages providing me these features? Of course with a good tutorial. I try to improve myself on R. But I am newbie
Great to see ambition like that.
I guess it really depends on what data you are starting with. If raw mass spec data, I'd recommend XCMS (https://www.bioconductor.org/packages/release/bioc/html/xcms.html). There are some tutorials on there and all over the web!
MSnbase (https://www.bioconductor.org/packages/release/bioc/html/MSnbase.html) works with xcms and contains a lot of useful functions.
I'd recommend taking a look at a recently published paper linked in here (http://www.metabolomics-forum.com/index.php?topic=1384.0). It covers a lot of what's available.