getInjectionPeak {proFIA} | R Documentation |
Determine an injection peak as an exponential modified gaussian function and a second order exponential corresponding to matrix effect to the most intense signals in an acquisition.
getInjectionPeak(xraw, bandlist, sec = 2, iquant = 0.95, gpeak = NULL, selIndex = NULL, scanmin = 1, scanmax = length(xraw@scantime), refinement = TRUE, graphical = FALSE)
xraw |
An xcmsRaw object as returned by |
bandlist |
A list of bands which can be used. Shall stay NULL in general use. bands will be determined automatically. |
sec |
A tolerance in sec to group the signals. |
iquant |
The maximum intensity intensity threshold under which the peaks would not be used for peak determination. |
gpeak |
An approximation of the injection peak, if NULL determining sizepeak.Geom will be used. |
selIndex |
A seleciton of index to make the regression. We recommend to let it to NULL. |
scanmin |
The first scan to consider for regression. |
scanmax |
The last scan to consider for regression. |
refinement |
Should the starting point of the regression be refined using the selected EICs. |
graphical |
shald the individually fitted components be plotted. |
A vector contaning the injection peak
if(require(plasFIA)){ #Getting the path of a file. path_raw <- list.files(system.file(package="plasFIA","mzML"),full.names=TRUE)[2] #Opening the file with xcms xraw <- xcmsRaw(path_raw) #Getting the injection scan gp <- determiningInjectionZone(xraw) #performing band detection. tbands <- findBandsFIA(xraw,ppm = 2,sizeMin = gp[3]-gp[1],beginning=gp[1],end=gp[2]) #Getting the injection peak vpeak <- getInjectionPeak(xraw,bandlist=tbands,gpeak=gp) plot(vpeak,type="l") }