inst/doc/mzR.R

In mzR: parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data)

## ----openraw------------------------------------------------------------------
library(mzR)
library(msdata)

mzxml <- system.file("threonine/threonine_i2_e35_pH_tree.mzXML",
                     package = "msdata")
aa <- openMSfile(mzxml)

## ----get header information---------------------------------------------------
runInfo(aa)
instrumentInfo(aa)
header(aa,1)

## ----plotspectrum-------------------------------------------------------------
pl <- peaks(aa,10)
peaksCount(aa,10)
head(pl)
plot(pl[,1], pl[,2], type="h", lwd=1)

## ----close the file-----------------------------------------------------------
close(aa)

## ----openid-------------------------------------------------------------------
library(mzR)
library(msdata)

file <- system.file("mzid", "Tandem.mzid.gz", package="msdata")
x <- openIDfile(file)

## ----metadata-----------------------------------------------------------------
mzidInfo(x)

## ----psms0--------------------------------------------------------------------
p <- psms(x)
colnames(p)

## ----psms1--------------------------------------------------------------------
m <- modifications(x)
head(m)

## ----psms2--------------------------------------------------------------------
scr <- score(x)
colnames(scr)

## ----label=sessioninfo, results='asis', echo=FALSE----------------------------
toLatex(sessionInfo())