sweep {hyperSpec}R Documentation

Sweep Summary Statistic out of an hyperSpec Object

Description

sweep for hyperSpec objects.

Usage

## S4 method for signature 'hyperSpec':
sweep(x, MARGIN, STATS, FUN = "-",
   check.margin = TRUE, ..., 
   short = NULL, user = NULL, date = NULL)

Arguments

x a hyperSpec object.
MARGIN direction of the spectra matrix that STATS goees along.
STATS the summary statistic to sweep out. Either a vector or a hyperSpec object.
FUN the function to do the sweeping, e.g. `-` or `/`.
check.margin If TRUE (the default), warn if the length or dimensions of STATS do not match the specified dimensions of x. Set to FALSE for a small speed gain when you know that dimensions match.
... further arguments for FUN
short, user, date handed over to logentry.

Details

Calls sweep for the spectra matrix.

sweep is useful for some spectra preprocessing, like offset correction, substraction of background spectra, and normalization of the spectra.

Value

A hyperSpec object.

Author(s)

C. Beleites

See Also

sweep

Examples

## 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)
corrected <- sweep (corrected, 1, factor, "/")
plot (corrected, "spcprctl5")

[Package hyperSpec version 0.95 Index]