NBSpliceRes-plotGeneResults: Method to obtain isoform's relative expression barplot for an...

In NBSplice: Negative Binomial Models to detect Differential Splicing

Description

plotGeneResults returns ggplot object which illustrates the isoform's relative expression in the two contrasted conditions.

Usage

plotGeneResults(myNBRes, gene, filterLowExpIso = TRUE,
    filterNotSignificant = TRUE, adjusted = TRUE, p.value = 0.05,
    group = TRUE)

## S4 method for signature 'NBSpliceRes'
plotGeneResults(myNBRes, gene, filterLowExpIso = TRUE,
    filterNotSignificant = TRUE, adjusted = TRUE, p.value = 0.05,
    group = TRUE)

Arguments

myNBRes	NBSpliceRes class object.
gene	Character indicating the gene name.
filterLowExpIso	Logical indicating if lower-expression isoforms should be filtered out.
filterNotSignificant	Logical indicating if not significant isoforms should be filtered out.
adjusted	Logical indicating if adjusted p values should be used.
p.value	Numeric value between 0 and 1 giving the required family-wise error rate or false discovery rate.
group	Logical indicating if isoforms bars should be stacked or not

Value

A ggplot object.

Note

see full example in NBSpliceRes-class

Author(s)

Gabriela A. Merino [e-mail] and Elmer A. Fernandez [e-mail]

See Also

NBSpliceRes

Other NBSpliceRes: GetDSGenes, GetDSResults, GetGeneResults, NBSpliceRes-class, NBSpliceRes-initialize, NBSpliceRes, myDSResults, plotRatiosDisp, plotVolcano

Examples

data(myDSResults, package="NBSplice")
gene<-results(myDSResults)[,"gene"][1]
##Plot gene results filtering low expressed isoforms
g<-plotGeneResults(myDSResults, gene)
if(interactive()){
g
}
##Plot gene results keeping low expressed isoforms
g<-plotGeneResults(myDSResults, gene, filterLowExpIso=FALSE)
if(interactive()){
g
}
##Plot isoform bar plots keeping low expressed isoforms
g<-plotGeneResults(myDSResults, gene, filterLowExpIso=FALSE, group=FALSE)
if(interactive()){
g
}

NBSplice documentation built on Nov. 8, 2020, 8:07 p.m.