calibrants: Class Representing a Set of Calibrants

Description Usage Arguments References See Also Examples

Description

A set of calibrants only contains a small number (typically 5 to 7) of proteins of known mass.

Class slots:

masses

A numeric vector of protein masses.

counts

An integer vector of protein counts/abundance.

Class extends:

proteins

by direct inclusion.

The class calibrants inherits all the methods of the class proteins.

Usage

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calibrants(masses, counts)

Arguments

masses

A positive numeric vector of protein masses, whose elements should be unique.

counts

A positive integer vector of protein counts/abundance, which should have the same length as masses.

References

Coombes, K.R., Koomen, J.M., Baggerly, K.A., Morris, J.S., Kobayashi, R., “Understanding the characteristics of mass spectrometry data through the use of simulation," Cancer Informatics, 2005(1):41–52, 2005.

See Also

proteins, spectrometer.

Examples

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## generate two protein samples 
cal1 <- calibrants(masses=c(1, 95, 190), counts=as.integer(c(500, 3000, 10000)))
cal2 <- calibrants(masses=10000+200*(0:3), counts=as.integer(c(12000, 4000, 2000, 1000)))

## print the synopsis of the protein samples 
cal1
cal2

## mix the protein samples 
cal <- cal1 + cal2

## visualize the calibrants 
plot(cal, type="h")

zeehio/msProcess documentation built on May 4, 2019, 10:15 p.m.