getDS: Extract lists of significant isoforms from Differentially...

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

Description

getDS creates lists of significant isoforms from Differentially Spliced Genes (DSG)

Usage

  getDS(Model, vars="all", rsq=0.4)

Arguments

Model	a IsoModel object
vars	argument of the get.siggenes function applied to isoforms
rsq	cut-off level at the R-squared value for the stepwise regression fit. Only isoforms with R-squared more than rsq are selected

Details

There are 3 possible values for the vars argument: "all", "each" and "groups". See get.siggenes.

Value

In the console a summary of the selection is printed.

Model	a IsoModel object to be used in the following steps
get2	a get.siggenes object to be used in the following steps
DSG	Names of the selected genes: Differentially Spliced Genes
DET	Names of the selected Isoforms: Differentally Expressed Transcripts
List0	a list with the names of Differentially Spliced Genes without Isoforms with R-squared higher than rsq
NumIso.by.gene	Number of selected Isoforms for each Differentially Spliced Gene

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

get.siggenes, 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)
Myget$DSG
Myget$DET

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.