Biomedical Engineering Reference
In-Depth Information
#-------------------------
# Install Package
#-------------------------
source('http://bioconductor.org/biocLite.R')
biocLite('xcms')
library(xcms)
#-------------------------
# Install Package
#-------------------------
source('http://bioconductor.org/biocLite.R')
biocLite('xcms')
library(xcms)
#------------------------------------------------
# set the working directory of R from the command
# line or alternatively from R Studio
#------------------------------------------------
setwd('C:/Your_Directory_Name')
#------------------------------------------------
# set the working directory of R from the command
# line or alternatively from R Studio
#------------------------------------------------
setwd('C:/Your_Directory_Name')
x1=xcmsRaw(fi lename='QC1_917_01.mzData', includeMSn=F)
x1
An 'xcmsRaw' object with 1000 mass spectra
x1=xcmsRaw(fi lename='QC1_917_01.mzData', includeMSn=F)
x1
An 'xcmsRaw' object with 1000 mass spectra
Time range: 0.4-839.7 seconds (0-14 minutes)
Mass range: 85.0023-899.9206 m/z
Intensity range: 127.735-49679200
Time range: 0.4-839.7 seconds (0-14 minutes)
Mass range: 85.0023-899.9206 m/z
Intensity range: 127.735-49679200
MSn data on 0 mass(es)
with 0 MSn spectra
Profi le method: bin
Profi le step: 1 m/z (816 grid points from 85 to 900 m/z)
MSn data on 0 mass(es)
with 0 MSn spectra
Profi le method: bin
Profi le step: 1 m/z (816 grid points from 85 to 900 m/z)
Memory usage: 28 MB
Memory usage: 28 MB
#-----------------------------------
#list the structure of the x1 object
#-----------------------------------
str(x1)
#-----------------------------------
#list the structure of the x1 object
#-----------------------------------
str(x1)
Formal class 'xcmsRaw' [package 'xcms'] with 20 slots
..@ env : <environment: 0x0000000009376678>
..@ tic : num [1:1000] 0 0 0 0 0 0 0 0 0 0 . . .
..@ scantime : num [1:1000] 0.411 1.554 2.835 4.144 5.464 . . .
..@ scanindex : int [1:1000] 0 1613 3309 4997 6774 8534 10273 11981
13691 15411 . . .
..@ polarity : Factor w/3 levels 'negative','positive',..: 3 3 3 3
3 3 3 3 3 3 . . .
..@ acquisitionNum : int [1:1000] 1 3 5 7 9 11 13 15 17 19 . . .
..@ profmethod : chr 'bin'
..@ profparam : list()
..@ mzrange : num [1:2] 85 900
..@ gradient : logi[0, 0 ]
..@ msnScanindex : int(0)
..@ msnAcquisitionNum : int(0)
..@ msnPrecursorScan : int(0)
..@ msnLevel : int(0)
..@ msnRt : num(0)
..@ msnPrecursorMz : num(0)
Formal class 'xcmsRaw' [package 'xcms'] with 20 slots
..@ env : <environment: 0x0000000009376678>
..@ tic : num [1:1000] 0 0 0 0 0 0 0 0 0 0 . . .
..@ scantime : num [1:1000] 0.411 1.554 2.835 4.144 5.464 . . .
..@ scanindex : int [1:1000] 0 1613 3309 4997 6774 8534 10273 11981
13691 15411 . . .
..@ polarity : Factor w/3 levels 'negative','positive',..: 3 3 3 3
3 3 3 3 3 3 . . .
..@ acquisitionNum : int [1:1000] 1 3 5 7 9 11 13 15 17 19 . . .
..@ profmethod : chr 'bin'
..@ profparam : list()
..@ mzrange : num [1:2] 85 900
..@ gradient : logi[0, 0 ]
..@ msnScanindex : int(0)
..@ msnAcquisitionNum : int(0)
..@ msnPrecursorScan : int(0)
..@ msnLevel : int(0)
..@ msnRt : num(0)
..@ msnPrecursorMz : num(0)
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