msCharge: Charge Detection

In zeehio/msProcess: Protein Mass Spectra Processing

Description

Find proteins that possibly have multiple charges. This is achieved by detecing proteins whose mz values are nearly exact multiples of others and hence potentially represent the same protein.

Usage

msCharge(x, ncharge=2:3, mz.precision=0.003,
    event="Charge Detection", ...)

Arguments

x	An object of class msSet with an existing element "peak.class".
...	Not used.
event	A character string denoting the name of the event to register with the (embedded) event history object of the input after processing the input data. Default: "Charge Detection".
mz.precision	A numeric value, used to construct the threshold when comparing the multiples of mz values. The default value is 0.003 because SELDI data is often assumed to have +/- 0.3% mass drift, i.e., a peak at mass w could represent a protein with a mass within the interval [w(1-0.003), w(1+0.003)].
ncharge	A numeric integer vector denoting the multiple charges of interest. All of its elements must be larger than 1.

Value

An object of class msSet with charge estimate attached as element "peak.charge".

See Also

msSet.

Examples

if (!exists("qcset")) data("qcset", package="msProcess")

## extract several spectra from the build-in
## dataset
z <- qcset[, 1:8]

## denoising
z <- msDenoise(z, FUN="wavelet", n.level=10, thresh.scale=2)

## local noise estimation
z <- msNoise(z, FUN="mean")

## baseline subtraction
z <- msDetrend(z, FUN="monotone", attach=TRUE)

## intensity normalization
z <- msNormalize(z)

## peak detection
z <- msPeak(z, FUN="simple", use.mean=FALSE, snr=2)

## peak alignment
z <- msAlign(z, FUN="cluster", snr.thresh=10,
    mz.precision=0.004)

## charge detection
z <- msCharge(z, ncharge=2:5, mz.precision=0.003)

## extract the peak.charge
z[["peak.charge"]]

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