add scan filters to readXICs()

fgcz / rawDiag

Brings Orbitrap mass spectrometry data to life; multi-platform, fast and colorful R package

https://bioconductor.org/packages/rawDiag

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add scan filters to readXICs() #41

Open tobiasko opened 5 years ago

tobiasko commented 5 years ago

Our current readXICs() does not support any scan filters. Actually the compiled c# code uses the hard coded filter:

Filter = "ms" that returns all scans. see line 1046 of fgcz_raw.cs

I think it would be cool to have an additional parameter for readXICs() that passes filters to the c# function.

tobiasko commented 5 years ago

The same applies for RT limits. see

"creating custom chromatograms"

in UsingRawFileReader

tobiasko commented 5 years ago

We should also adapt the XIC object structure. Currently we return

> str(X[[1]])
List of 4
 $ mass       : num 487
 $ times      : num [1:998] 0.604 0.631 0.659 0.685 0.688 ...
 $ intensities: num [1:998] 565 1684 704 13480 6214 ...
 $ filename   : chr "20180717_006_tSIM_demo.raw"
 - attr(*, "class")= chr [1:2] "list" "XIC"
> otype(X[[1]])
[1] "S3"
> class(X[[1]])
[1] "list" "XIC"

without attributes for tolerance, RT limits, scan filters used to construct the object.

tobiasko commented 5 years ago

Another thing that comes to my mind: Is readXIC() a good name, or should it simply be XIC() like the class? This would follow the typical S3 constructor function style.