Using xcms and Spectra package

[felipe-mansoldo]

Dear all, From what I understand, the connection between xcms and Spectra is made with MsExperiment objects. I'm trying to reproduce the xcmsTutorials but with fictitious data in Spectra, but I'm having difficulties when linking the linkSampleData.

Please see this minimal example:

library(xcms)
library(MsExperiment)
library(Spectra)

#' fake  MS data
mz <- c(56.0494, 69.0447, 83.0603, 109.0395, 110.0712,
        111.0551, 123.0429, 138.0662, 195.0876)
int <- c(0.459, 2.585, 2.446, 0.508, 8.968, 0.524, 0.974, 100.0, 40.994)

sv <- data.frame(msLevel = 1L, polarity = 1L, rtime=1)
sv <- rbind(sv, data.frame(msLevel = 1L, polarity = 1L, rtime=2))
sv <- rbind(sv, data.frame(msLevel = 1L, polarity = 1L, rtime=3))

sv$mz <- list(mz)
sv$intensity <- list(int)

sv$dataOrigin = normalizePath("abstractFile.mzML")

sps_sv <- Spectra(sv)
sps_sv

msexp <- MsExperiment()
msexp

spectra(msexp) <- sps_sv

sampleData(msexp)$raw_file <- sps_sv$dataOrigin

the error:

> sampleData(msexp)$raw_file <- sps_sv$dataOrigin
Error in `[[<-`(`*tmp*`, name, value = c("C:\\Users\\User\\testing\\abstractFile.mzML",  : 
  3 elements in value to replace 0 elements

Is there another way to use xcms functions with Spectra data? thanks