Print Page - How to access data returned by getEIC?

Title: How to access data returned by getEIC?
Post by: allend on July 10, 2014, 09:40:16 AM

I am a dill and a dodo with failing Google fu,

I can open a data file in R with

filename <- "#4606.mzXML"
xraw <- xcmsRaw(filename)

and get an extracted ion chromatogram with

Code: [Select]

mzr <- cbind(179.9,180.3)
rtr <- cbind(397,1560.3)
eicm <- getEIC(xraw, mzrange = mzr, rtrange = rtr)

but for further processing I would now like to access the values for 'rt' and 'intensity' as displayed by

Code: [Select]

> attr(eicm,"eic")
$xcmsRaw
$xcmsRaw[[1]]
              rt  intensity
   [1,]  397.022       1425
   [2,]  397.241      13700
...
[5510,] 1560.069          0
[5511,] 1560.288      36000

Could somebody please help with the required voodoo?

TIA

Title: Re: How to access data returned by getEIC?
Post by: allend on July 11, 2014, 12:58:52 AM

I have answered my own question after a good night's sleep.

Code: [Select]

temp <- attr(eicm,"eic")
rtime <- temp$xcmsRaw[[1]][,1] # get rt's
intensity <- temp$xcmsRaw[[1]][,2] # get intensities

Sorry for the noise.

Metabolomics Society Forum

Software => R => XCMS => Topic started by: allend on July 10, 2014, 09:40:16 AM