getDSPatterns: Lists of genes with Isoforms in different clusters

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

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, [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

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")

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