Question: visualizing top differentially spliced genes
1
3.7 years ago by
osa.zuta40
United States
osa.zuta40 wrote:

Hello,

I am using voom/limma to detect differential splicing via diffSplice, with visualization via plotSplice. I am trying to figure out how to make a heatmap of relative exon usage for my top hits, analagous to a heatmap of expression which illustrates the top hits of ordinary differential expression. This heatmap  should clearly show the change in relative logFC for a given exon of the particular gene which is called differentially spliced.

So, for example suppose I have (for some expression cutoff is_expr) an exon count matrix ecounts over some samples, then:

dge_exon <- DGEList( counts = ecounts, genes = e_annotation)

dge_exon <- dge_exon[is_expr,]

dge_exon <- calcNormFactors(dge_exon)

v_exon <- voom( dge_exon, design)
fx <- eBayes(lmFit(v_exon, design))
ex <- diffSplice(fx)

and I want to plot relative exon usage as a heatmap across all my samples using the top few hits in ex. How do I compute this relative usage matrix across all my samples? Would it be something like

eusage <- aggregate( v_exon$E, by = list(as.matrix(v_exon$genes\$GeneID)), function(x) x/sum(x) )

zo