getDSPatterns: Lists of genes with Isoforms in different clusters
In maSigPro: Significant Gene Expression Profile Differences in Time Course Gene Expression Data

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

getDSPatterns is a function that makes a list with the names of genes identified with tableDS function.

1	getDSPatterns(tableDS, Cluster.Major, Cluster.minor)

`tableDS`	a `tableDS` object
`Cluster.Major`	Number of the cluster where the major isoform belongs to
`Cluster.minor`	Number(s) of the cluster(s) where the minor isoform(s) belongs to (see details)

When minor isoforms belong to different clusters, tableDS codifies them using "&". For instance: clusters 1 and 2, will be represented as "1&2". In such cases quotation marks must be used (see examples). When minor isoforms are only in one cluster there is no need to use quotation marks.

A vector with the names of the genes.

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.

tableDS, 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)
see <- seeDS(Myget, cluster.all=FALSE, k=6)
table <- tableDS(see)
table$IsoTable

getDSPatterns(table, 1, 4) 
getDSPatterns(table, "1", "4") #will give the same result.

getDSPatterns(table, 1, "1&5")