dataProcessing {LipidMS} | R Documentation |
Process mzXML files: peak-picking using enviPick and deisotoping using an adaptation of the CAMERA algorithm.
dataProcessing( file, mslevel, polarity, dmzgap = 50, drtgap = 25, ppm = TRUE, minpeak, maxint = 1e+09, dmzdens, drtdens = 20, merged = FALSE, drtsmall, drtfill = 5, drttotal = 100, recurs = 4, weight, SB, SN = 2, minint, ended = 2, removeIsotopes = TRUE, rttolIso = 2, ppmIso = 20 )
file |
path of the mzXML input file. |
mslevel |
numeric value indicating if data belongs to level 1 (fullMS) or level 2 (MS/MS). |
polarity |
character value: negative or positive. |
dmzgap |
enviPick parameter. 50 by default. |
drtgap |
enviPick parameter. 25 by default. |
ppm |
logical value. TRUE if dmzdens was set in ppm and FALSE if it was in as an absolute value. TRUE by default. |
minpeak |
minimum number of measurements required within the RT window of drtsmall. Optional. By default, 5 when mslevel = 1 and 4 when mslevel = 2. |
maxint |
EIC cluster with measurements above this intensity are kept, even if they do not fulfill minpeak. 1E9 by default. |
dmzdens |
maximum measurement deviation (+/-) of m/z from its mean within each EIC. Optional. By default, 15 when mslevel = 1 and 30 when mslevel = 2. |
drtdens |
RT tolerance for clustering. Optional. 20 by default. |
merged |
merge EIC cluster of comparable m/z. Logical. FALSE by default. |
drtsmall |
peak definition - RT window of a peak. Optional. By default, 100 when mslevel = 1 and 30 when mslevel = 2. |
drtfill |
maximum RT gap length to be filled. 5 by default. |
drttotal |
maximum RT length of a single peak. 100 by default. |
recurs |
maximum number of peaks within one EIC. 3 by default. |
weight |
weight for assigning measurements to a peak. Optional. By default, 1 when mslevel = 1 and 2 when mslevel = 2. |
SB |
signal-to-base ratio. Optional. By default, 3 when mslevel = 1 and 2 when mslevel = 2. |
SN |
signal-to-noise ratio. 2 by default. |
minint |
minimum intensity of a peakr. Optional. By default, 1000 when mslevel = 1 and 100 when mslevel = 2. |
ended |
within the peak detection recursion set by argument recurs, how often can a peak detection fail to end the recursion?. 2 by default. |
removeIsotopes |
logical. If TRUE, only isotopes identified as M+0, are kept when mslevel = 1, and M+0 or unknown when mslevel = 2. TRUE by default. If FALSE, an additional column is added to the peak list to inform about isotopes. |
rttolIso |
numeric. Time windows for isotope matching. |
ppmIso |
numeric. Mass tolerance for isotope matching. |
This function executes 2 steps: 1) peak-picking using enviPick package and 2) it searches isotopes using an adaptation of the CAMERA algorithm. If mslevel = 1 and remove isotopes is set as TRUE, only ions with more than 1 isotope are kept.
List with two data frames: peaklist, with 4 columns (m.z, RT, int, and peakID) and rawScan, with all the scans information in 5 columns (m.z, RT, int, peakID and Scan). PeakID columns links both data frames: extracted peaks and raw data. The Scan column indicates the scan number (order) to which each row of the rawScans data frame belong.
M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
https://cran.r-project.org/web/packages/enviPick/index.html
Kuhl C, Tautenhahn R, Boettcher C, Larson TR ans Neumann S (2012). "CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography-mass spectrometry data sets." Analytical Chemistry, 84, pp. 283-289. htto://pubs.acs.org/doi/abs/10.1021/ac202450g.
## Not run: dataProcessing("input_file.mzXML", mslevel = 1, polarity = "positive") ## End(Not run)