Just to be sure you're aware, there are packages for chromatograpy and mass
spec data in Bioconductor. Like xcms. Don't think any will directly address
your problem, but they might be useful.
Michael
On Tue, Feb 17, 2009 at 5:44 AM, bartjoosen wrote:
>
> Hi,
>
> I'm trying to match peaks between chromatographic runs.
> I'm able to match peaks when they are chromatographed with the same method,
> but not when there are different methods are used and spectra comes in to
> play.
>
> While searching I found the ALS package which should be usefull for my
> application, but I couldn't figure it out.
>
> I made some dummy chroms with R, which mimic my actual datasets, to play
> with, but after looking at the manuals of ALS, I'm affraid I can't get the
> job done. Can someone put me on the right way?
>
> Here is my code to generate the dummy chroms, which also plots the 2 chroms
> and the spectra of the 3 peaks:
>
> #2D chromatogram generation
> par(mfrow=c(3,1))
> time <- seq(0,20,by=0.05)
> f <- function(x,rt) dnorm((x-rt),mean=0,sd=rt/35)
> c1 <- f(time,6.1)
> c2 <- f(time,5.6)
> c3 <- f(time,15)
> plot(c1+c2+c3~time,type="l",main="chrom1")
>
> #spectrum generation
> spectra <- function(x,a,b,c,d,e) a + b*(x-e) + c*((x-e)^2) + d*((x-e)^3)
> x <- 220:300
> s1 <- spectra(x,(-194.2),2.386,(-0.009617),(1.275e-05),0)
> s2 <- spectra(x,(-1.054e02),1.3,(-5.239e-03),(6.927e-06),-20)
> s3 <- spectra(x,(-194.2),2.386,(-0.009617),(1.275e-05),20)
>
> chrom1.tot <-
> data.frame(time,outer(c1,s1,"*")+outer(c2,s2,"*")+outer(c2,s2,"*"))
> names(chrom.tot)[-1] <- x
>
> #generation of chromatogram 2
> c1 <- f(time,2.1)
> c2 <- f(time,4)
> c3 <- f(time,8)
> plot(c1+c2+c3~time,type="l",main="chrom2")
>
> chrom2.tot <-
> data.frame(time,outer(c1,s1,"*")+outer(c2,s2,"*")+outer(c2,s2,"*"))
> names(chrom.tot)[-1] <- x
>
> plot(s1~x,type="l",main="spectra")
> lines(s2~x,col=2)
> lines(s3~x,col=3)
>
> Thanks for your time
>
> Kind Regards
>
> Bart
> --
> View this message in context:
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> Sent from the R help mailing list archive at Nabble.com.
>
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