tableDS: Identification of Mayor and minor Isoforms in the clusters

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

Description

tableDS identifies for each Differentialy Spliced Gene (DSG) the clusters where their isoforms belong to, labelling gene transcripts as mayor (or most expressed) and minor.

Usage

 tableDS(seeDS)

Arguments

seeDS

a seeDS object

Details

This table includes DSG with 2 or more Isoforms. Mono isoform genes are useful to determine the trends of the cluster. However, as they have only one Isoform, there is not the possibility of comparing minor and major DETs.

Value

IsoTable	A classification table that indicates the distribution of isoforms across diferent clusters
IsoClusters	A data.frame with genes in rows and two columns: first indicates the number of cluster of the major isoform and second the number(s) of cluster(s) of the minor isoforms.

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

seeDS, 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

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