msPrepare: Convert an msList Object to an msSet Object

In zeehio/msProcess: Protein Mass Spectra Processing

Description

Converts an msList object to an msSet object by truncating the spectra to the mass range of interest, interpolating the spectra to a common set of m/z values, and transforming the intensity values if specified.

Usage

msPrepare(x, mass.min=1500, transform=NULL, data.name = NULL)

Arguments

x	An object of class msList.
mass.min	A numeric value denoting the lowest mass (in Dalton) of interest. The portion of the spectra below this value will be removed. The low mass region is generally considered suspicious as matrix contamination may be a problem. Default: 1500.
transform	A function to be used to transform the intensity values. The main purpose of the transformation is to reduce the variance of the intensity values and to stabilize the noise component of the spectra. Some possible choices are logarithm (log), square root (sqrt) and cube root. The default is not to perform any tranformation. Default: NULL (no transform).
data.name	name for the data. Default: deparseText(substitute(x)).

Value

An object of class msSet that has the same number of spectra as in the input msList object x.

See Also

msList, msSet, msNormalize.

Examples

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

## extract several spectra from the build-in 
## dataset qclist 
zList <- qclist[1:8]

## convert the subset to an msSet object 
cbrt <- function(x) x^(1/3)
zSet <- msPrepare(zList, mass.min=950, transform=cbrt)

## visualize a portion of the spectra 
plot(zSet, subset=NULL, xlim=c(13000, 17000), offset=0.5)

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