assessPuritySingle {msPurity} | R Documentation |
Given a filepath to an mzML file the precursor purity for any MS/MS scans will be outputed into a dataframe
assessPuritySingle(filepth, fileid = NA, mostIntense = FALSE, nearest = TRUE, offsets = NA, cores = 1, plotP = FALSE, plotdir = NULL, interpol = "linear", iwNorm = FALSE, iwNormFun = NULL, ilim = 0, mzRback = "pwiz", isotopes = TRUE, im = NULL)
filepth |
character; mzML file path for MS/MS spectra |
fileid |
numeric; adds a fileid column (primarily for internal use for msPurity) |
mostIntense |
boolean; True if the most intense peak is used for calculation. False if the centered peak is used |
nearest |
boolean; True if the peak selected is as the nearest MS1 scan. If False then the preceding scan is used |
offsets |
vector; Overide the isolation offsets found in the mzML filee.g. c(0.5, 0.5) |
cores |
numeric; Number of cores to use |
plotP |
boolean; If TRUE a plot of the purity is to be saved |
plotdir |
vector; If plotP is TRUE plots will be saved to this directory |
interpol |
character; Type of interolation to be performed "linear", "spline" or "none" |
iwNorm |
boolean; If TRUE then the intensity of the isolation window will be normalised based on the iwNormFun function |
iwNormFun |
function; A function to normalise the isolation window intensity. The default function is very generalised and just accounts for edge effects |
ilim |
numeric; All peaks less than this percentage of the target peak will be removed from the purity calculation, default is 5% (0.05) |
mzRback |
character; Backend to use for mzR parsing |
isotopes |
boolean; TRUE if isotopes are to be removed |
im |
matrix; Isotope matrix, default removes C13 isotopes (single, double and triple bonds) |
a dataframe of the purity score of the ms/ms spectra
filepth <- system.file("extdata", "lcms", "mzML", "LCMSMS_1.mzML", package="msPurityData") puritydf <- assessPuritySingle(filepth)