hyperSpec (version 0.98-20120224)

sweep: Sweep Summary Statistic out of an hyperSpec Object sweep for hyperSpec objects.

Description

Calls sweep for the spectra matrix.

Usage

## S3 method for class 'hyperSpec':
sweep(x, MARGIN, STATS, FUN = "-",
    check.margin = TRUE, ..., short = "sweep", 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.

hyperSpec offers a non-standard convenience function: if STATS is a function, this function is applied first (with the same MARGIN)

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.

Value

• A hyperSpec object.

Details

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

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)
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))