readRaw {ptairMS} | R Documentation |
readRaw
reads a h5 file with rhdf5 library, and calibrates the
mass axis with mzCalibRef
masses each calibrationPeriod
seconds. It returns a ptrRaw-class
S4 object,
that contains raw data.
readRaw( filePath, calib = TRUE, mzCalibRef = c(21.022, 29.013424, 41.03858, 60.0525, 203.943, 330.8495), calibrationPeriod = 60, tolCalibPpm = 70, maxTimePoint = 900 )
filePath |
h5 absolute file path full name. |
calib |
boolean. If true, an external calibration is performed on
the |
mzCalibRef |
calibration parameter. Vector of exact theoretical masses values of an intensive peak without overlapping. |
calibrationPeriod |
in second, coefficient calibration are estimated
for each sum spectrum of
|
tolCalibPpm |
calibration parameter. The maximum error tolerated in ppm.
A warning appears for error greater than |
maxTimePoint |
number maximal of time point to read |
a ptrRaw object, including slot
rawM the data raw matrix, in count of ions
mz the mz axis
time time acquisition in second
library(ptairData) filePathRaw <- system.file('extdata/exhaledAir/ind1', 'ind1-1.h5', package = 'ptairData') raw <- readRaw(filePath=filePathRaw, mzCalibRef=c(21.022, 60.0525), calib=FALSE)