RIcorrect {TargetSearch} | R Documentation |
This function reads from CDF files, finds the apex intensities, converts the retention time to retention time index (RI), and writes RI corrected text files (a.k.a. RI files).
RIcorrect(samples, rimLimits = NULL, massRange = NULL, Window, IntThreshold, pp.method = "ppc", showProgressBar = FALSE, baseline = FALSE, baseline.opts = NULL )
samples |
A |
rimLimits |
A |
massRange |
Deprecated. It is completely ignored but it is kept for compatibility with old scripts. |
Window |
The window used for smoothing. The number of points actually used
is |
IntThreshold |
Apex intensities lower than this value will be removed from the RI files. |
pp.method |
Peak picking method. Options are "smoothing", "gaussian" and "ppc". See details. |
showProgressBar |
Logical. Should the progress bar be displayed? |
baseline |
Logical. Should baseline correction be performed? |
baseline.opts |
A list of options passed to |
.
There are three pick picking methods available: "ppc", "smoothing", "gaussian".
The "ppc" method (default) implements the peak detection method described in the ppc
package. It looks for the local maxima within a 2*Window + 1
scans for
every mass trace.
The "smoothing" method calculates a moving average of 2*Window + 1
points
for every mass trace. Then it looks for a change of sign (from positive to negative) of
the difference between two consecutive points. Those points will be returned as
detected peaks.
The "gaussian" method behaves similar to the "smoothing" method, but instead a gaussian smoother is used instead of the moving average.
To work out a suitable Window
value, the following might be useful:
Window = (SR * PW - 1) / 2
, where SR is the scan rate of the MS instrument and
PW is the peak width. Because Window
is an integer, the resulting value must be
rounded. For example, for SR = 20 scans per second, a PW = 1.5 seconds, then
Window
= 14.5, which can be rounded to 15.
The RI file type is determined by the output of fileFormat
method applied to the tsSample
input object. To
choose between the available formats ("binary" and "text"), select it
with fileFormat
method before calling RIcorrect
.
A retention time matrix of the found retention time markers. Every column represents a sample and rows RT markers.
Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig
ImportSamples
, ImportFameSettings
,
NetCDFPeakFinding
, FAMEoutliers
,
tsSample
, tsRim
.
require(TargetSearchData) # import refLibrary, rimLimits and sampleDescription. data(TSExample) # get the CDF files cdfpath <- file.path(find.package("TargetSearchData"), "gc-ms-data") cdfpath list.files(cdfpath) # update the CDF path CDFpath(sampleDescription) <- cdfpath # run RIcorrect (massScanRange = 85-320; Intensity Threshold = 50; # peak detection method = "ppc", window = 15) RImatrix <- RIcorrect(sampleDescription, rimLimits, Window = 15, pp.method = "ppc", IntThreshold = 50) # you can try other parameters and other peak picking algorithm. RImatrix <- RIcorrect(sampleDescription, rimLimits, Window = 15, pp.method = "smoothing", IntThreshold = 10) RImatrix <- RIcorrect(sampleDescription, rimLimits, Window = 15, pp.method = "ppc", IntThreshold = 100)