isobar-plots: IBSpectra plots

In isobar: Analysis and quantitation of isobarically tagged MSMS proteomics data

Description

Various plots are implement to assure data quality, and accompany preprocessing and analysis.

reporterMassPrecision

reporterMassPrecision(x):

Calculates and displays the deviation from the 'true' tag mass - as specified in the IBSpectra object - of each channel.

reporterIntensityPlot

reporterIntensityPlot(x):

Displays boxplots of intensity of channels before and after normalization - useful to check the result of normalization.

raplot

raplot(x,...):

Ratio-Absolute intensity plot - will be deprecated by maplot

x

IBSpectra object

...

Parameters to plot function.

plotRatio

plotRatio(x,channel1,channel2,protein,...):

Plots abundances of one protein

x

IBSpectra object

channel1

channel2

protein

...

Parameters to plot function.

maplot

maplot(x,channel1,channel2,...):

Creates a ratio-versus-intensity plot.

x

IBSpectra object.

maplot2

maplot2():

Author(s)

Florian P. Breitwieser, Jacques Colinge

See Also

IBSpectra, isobar-preprocessing isobar-analysis

Examples

data(ibspiked_set1)
maplot(ibspiked_set1,main="IBSpiked, not normalized")
maplot(normalize(ibspiked_set1),main="IBSpiked, normalized")

isobar documentation built on Nov. 8, 2020, 7:48 p.m.