IsoPlot: Plotting the isoform profiles of a specific gene by groups
In maSigPro: Significant Gene Expression Profile Differences in Time Course Gene Expression Data

Description Usage Arguments Details Value Author(s) References See Also Examples

This function makes a plot with the isoforms of a specific gene splitting the different experimental groups.

1	IsoPlot(get, name, only.sig.iso=FALSE, ylim=NULL, xlab = "Time", ylab = "Expression value", points=TRUE, cex.main=3,cex.legend=1.5)

`get`	a `getDS` object a cluster of flat Isoform
`name`	Name of the specific gen to show in the plot
`only.sig.iso`	TRUE when the plot is made only with statistically significant isoforms.
`ylim`	Range of the y axis of the desired plot. If it is NULL it will be computed automatically.
`xlab`	label for the x axis
`ylab`	label for the y axis
`points`	TRUE to plot points and lines. FALSE to plot only lines.
`cex.main`	graphical parameter magnification to be used for main
`cex.legend`	graphical parameter magnification to be used for legend

The plot can be made with all the available isoforms or only with the statistilly significant ones.

Plot of isoform profiles of a specific gene by groups.

Maria Jose Nueda, mj.nueda@ua.es

Nueda, M.J., Martorell, J., Marti, C., Tarazona, S and Conesa, A. 2017. Identification and visualization of differential isoform expression in RNA-Seq time series. In preparation.

Nueda, M.J., Tarazona, S., Conesa, A. 2014. Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series. Bioinformatics, 30, 2598-602.

Conesa, A., Nueda M.J., Alberto Ferrer, A., Talon, T. 2006. maSigPro: a Method to Identify Significant Differential Expression Profiles in Time-Course Microarray Experiments. Bioinformatics 22, 1096-1102.

getDS, IsoModel

data(ISOdata)
data(ISOdesign)
mdis <- make.design.matrix(ISOdesign)
MyIso <- IsoModel(data=ISOdata[,-1], gen=ISOdata[,1], design=mdis, counts=TRUE)
Myget <- getDS(MyIso)

IsoPlot(Myget,"Gene1005",only.sig.iso=FALSE,cex.main=2,cex.legend=1)