getDSPatterns {maSigPro} | R Documentation

## Lists of genes with Isoforms in different clusters

### Description

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

### Usage

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

### Arguments

`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)

### 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.

### Value

A vector with the names of the genes.

### Author(s)

Maria Jose Nueda, mj.nueda@ua.es

### 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

`tableDS`, `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)
    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")

[Package maSigPro version 1.64.0 Index]