PodiumChange: Detection of Genes with switchs of their major isoforms

In mjnueda/maSigPro: Significant Gene Expression Profile Differences in Time Course Gene Expression Data

Description

This function provides lists of genes that have different Major isoforms (most expressed) when different intervals of the experimental conditions are considered.

The subrange of the experimental conditions can be chosen as a specific point, all the points of a specific experimental group or at any point.

Usage

PodiumChange(get, only.sig.iso=FALSE,  comparison=c("any",
"groups","specific"), group.name="Ctr", time.points=0)

Arguments

get	a getDS object a cluster of flat Isoform
only.sig.iso	TRUE when changes are looked for only through statistically significant isoforms.
comparison	Type of search to do: any, groups or specific (see details).
group.name	required when comparison is "specific".
time.points	required when comparison is "specific".

Details

There are 3 possible values for the comparison argument:

"any": Detects genes with Major Isoform changes in at least one experimental condition.

"groups": Detects genes with different Major Isoform for different experimental groups.

"specific": Detects genes with Major Isoform changes in a specific time interval, especified in time.points argument and a specific experimental group, especified in group.name argument.

Value

L	Names of the genes with PodiumChange Isoforms
data.L	Data values of all the isoforms belonging to the genes in L
gen.L	gen vector with the name of the gene of each isoform
edesign	matrix describing experimental design needed to visualize PodiumChange selection with IsoPlot function. It is the input of make.design.matrix.

Author(s)

Maria Jose Nueda, [e-mail]

References

Nueda, M.J., Martorell, J., Marti, C., Tarazona, S., Conesa, A. 2018. Identification and visualization of differential isoform expression in RNA-seq time series. Bioinformatics. 34, 3, 524-526. 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.

See Also

see.genes, IsoModel

Examples

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

PC <- PodiumChange(Myget, only.sig.iso=TRUE,
comparison="specific", group.name="Group2", time.points=c(18,24))
PC$L

mjnueda/maSigPro documentation built on Dec. 11, 2020, 12:21 a.m.