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Topics - gooooh

1
XCMS / export XCMS2 fragments
Hi,

I used xcms2 on my lcmsms and have successfully executed the following commands.

Code: [Select]
#Load all libraries
library(xcms)

#Create and spacify filepath
path <- "G:/msms"
files <- list.files(path, full.names=TRUE, pattern="cp.mzXML", recursive = TRUE)


xrawctrl <- xcmsRaw(files[1], includeMSn = TRUE)
peaks <- findPeaks(xrawctrl, method="MS1")
xs <- xcmsSet(files, method="MS1")
xfrag <- xcmsFragments(xs)

Code: [Select]
> xfrag
An "xcmsFragments" object with  5819  peaks in 912 Spectra
From Level 1 to 2 Number of Samples:  1 .

Sample 1 :
    646 Peaks in Level 1 
    5173 Peaks in Level 2 

Memory usage: 0.402 MB

I know that the searchmetlin is no longer available in xcms2. May i know how to extract the fragments with the parent ions out so i can do compound annotations  ? I have tried the code as below but couldn't get it out.

Code: [Select]
xfragdata <- groupval(xfrag, value = "into")
write.csv(xfrag, file="xfrag.csv")


Thank you.

Regards.
2
XCMS / Error when executing xcmsset
Hi,

I'm very new in R and using xcms for analysis.
I have LCMS data in mzxml which contains two groups (A and B) in seperate sub directories. for example, inside folder "neg" contains two subfolders "A" and "B".
i have loaded the library and create the path to where my file contains using the command as below.
When i execute the xcmsset i get error.

Code: [Select]
library(BiocStyle)
library(multtest)
library(xcms)
path <- "G://mzxml/np/neg"
files <- system.file(path, full.names=TRUE, pattern="mzxml", recursive = TRUE)
xset <- xcmsSet(files,
                method="centWave",
                ppm = 10,
                peakwidth = c(20, 50),
                snthresh = 6,
                prefilter = c(3, 100),
                integrate = 1,
                mzdiff = 0.01
)

The error is as below.

Code: [Select]
Error in if (any(info$isdir)) { : missing value where TRUE/FALSE needed

May i know is it caused by in-correct filepath or something else ?

Thank you

Regards,
goo