msList: S3 Class Representing a List of Spectra with Possibly...
In zeehio/msProcess: Protein Mass Spectra Processing

Description S3 METHODS See Also Examples

An msList object is a list of matrices with each matrix representing a spectrum. Each matrix in the list has two columns. The first column is named "mz" and contains the m/z values. The second column is named "intensity" and contains the intensity values. The list has also an attribute named "type", which is of type factor and contains the classification labels for the spectra. An object of this class is usually generated from the function msImport() in package proteome.

[

extract or replace parts of an msList object.

Usage: x[i]

x: an msList object.
i: a subscript expression used to identify the spectra to extract or replace.

merge

merges multiple msList objects.

Usage: merge(...)

...: msList objects.

plot

plot a single spectrum from an msList object.

Usage: plot(x, index=1, type="l", add=FALSE, ...)

x: an msList object.
index: a single numeric value or character string specifying the spectrum to be plotted. The default is 1.
type: a single character specifying the type of plot. see fucntion par for details. The default is "l"
add: A logical value. If TRUE, the plot is added using the current par() layout. Otherwise a new plot is produced. Default: FALSE.
...: other graphical parameters passed to the plot function.

print

prints an msList object.

Usage: print(x, justify="left", sep=":", ...) or x

x: an msList object.
justify: a character string giving the justification of the numbers relative to each other. The choices are "none", "left", "right" and "decimal". Only the first letter needs to be given.
sep: a character string to be inserted between text and values. The default is a colon.

summary

provides a synopsis of an msList object.

Usage: summary(x)

x: an msList object.

msSet.

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

## print an msList object 
qclist

## print the synopsis of an msList object 
summary(qclist)

## plot the first spectrum from an msList object 
plot(qclist, index=1)