Sweep Summary Statistic out of an hyperSpec Object sweep for hyperSpec objects.
Calls sweep for the spectra matrix.
## S4 method for signature 'hyperSpec' sweep(x, MARGIN, STATS, FUN = "-", check.margin = TRUE, ...)
x |
a |
MARGIN |
direction of the spectra matrix that |
STATS |
the summary statistic to sweep out. Either a vector or a
hyperSpec offers a non-standard convenience function: if |
FUN |
the function to do the sweeping, e.g. '-' or '/'. |
check.margin |
If |
... |
further arguments for |
sweep is useful for some spectra preprocessing, like offset
correction, substraction of background spectra, and normalization of the
spectra.
A hyperSpec object.
C. Beleites
## Substract the background / slide / blank spectrum # the example data does not have spectra of the empty slide, # so instead the overall composition of the sample is substracted background <- apply (chondro, 2, quantile, probs = 0.05) corrected <- sweep (chondro, 2, background, "-") plot (corrected, "spcprctl5") ## Offset correction offsets <- apply (chondro, 1, min) corrected <- sweep (chondro, 1, offsets, "-") plot (corrected, "spcprctl5") ## Min-max normalization (on max amide I) # the minimum is set to zero by the offset correction. factor <- apply (corrected, 1, max) mm.corrected <- sweep (corrected, 1, factor, "/") plot (mm.corrected, "spcprctl5") ## convenience: give function to compute STATS: mm.corrected2 <- sweep (corrected, 1, max, "/") plot (mm.corrected2) ## checking stopifnot (all (mm.corrected2 == mm.corrected))
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