In jmbadia/GcxGctools: Tools for GCxGc data

GcxGctools is a package made with the aim of working with GcxGc raw data. The package is composed of a few functions, but only precook_measures() and draw_TICspectrum() should be used as a matter of fact; the other functions are only for rare occasions .

Usual workflow

blablabla.. you know how the package works but you only need a little workflow remembrance?. Ok:

1. Precook the mesures if you need to...

precook_measures(cdf_folder="C:/esborrar_mesuresGcxGc/mesures_Berkely_Noelia", #directory with the ncdf4 files
                 massestoavoid=c(43,61,70,73,88,207,208,209,210,281), #masses we don't want on the altered TIC
                 tmod=5,#modulation time
                 t2in=1, #Initial time of the second cromatographic column to start obtaining measures. By default is 0
                 t2out=5)#Final time of the second cromatographic column to end obtaining measures. By default is the modulation time

1. ...and draw the TIC you want (altered or not)

draw_TICspectrum(cdf_folder="C:/esborrar_mesuresGcxGc/mesures_Berkely_Noelia",#directory with the precooked files
                 normalizationfactor<-c(0.043, 1.725,0.371,0.055,0.034,0.062), 
                 samplestodraw_altTIC = list(c(2,-3),2,3),#samples whose altered TIC must be drawed
                 samplestodraw_NaltTIC = list(1,2),#samples whose non-altered TIC must be drawed
                 colors=c("red","black","#fdc086","grey","#7fc97f") )

I'm a newbie. How should I begin?

Start with a folder with yor cdf files, each file corresponding to a measure or sample. Keep the file names as short as possible (D1.cdf, D2.cdf, Y2.cdf); this names will be used to write legends on graphics.

Also it's important to note the alphabetical order of the files. You will be referring to each measure according to its position in that order. In the following example the funcion is asking to draw the second and third file (sample) of the directory.

draw_TICspectrum(...,samplestodraw_altTIC = list(2,3))

Precook? WTF is precook?

There are a lot of preprocessing algorithms needs to be done each time we have to work with measures. In order to save time measures are preprocessed (precooked) only once and the result saved on temporary files. The package's functions will read the already preprocessed data from those temporary files.

So the first think needed to be done in a new measure's directory is....right, you have to precook the measures. e.g.

precook_measures(cdf_folder="C:/esborrar_mesuresGcxGc/mesures_Berkely_Noelia", #directory with the ncdf4 files
                 massestoavoid=c(43,61,70,73,88,207,208,209,210,281), #masses we don't want on the altered TIC
                 tmod=5,#modulation time
                 t2in=1, #Initial time of the second cromatographic column to start obtaining measures. By default is 0
                 t2out=5)#Final time of the second cromatographic column to end obtaining measures. By default is the modulation time

Use ?precook_measures for more info

Let's draw it

Once we have the precooked files, just draw the measures using draw_TICspectrum(). To give an example,

library(GcxGctools)
draw_TICspectrum(cdf_folder="C:/esborrar_mesuresGcxGc/mesures_Berkely_Noelia",#directory with the precooked files
                 normalizationfactor<-c(0.043, 1.725,0.371,0.055,0.034,0.062), 
                 samplestodraw_altTIC = list(c(2,-3),2,3),#samples whose altered TIC must be drawed
                 samplestodraw_NaltTIC = list(1,2),#samples whose non-altered TIC must be drawed
                 colors=c("red","black","#fdc086","grey","#7fc97f") )

Use ?draw_TICspectrum for more info

jmbadia/GcxGctools documentation built on May 19, 2019, 4:06 p.m.