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


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) ) 

Thank you in advance for your help!






ADD COMMENTlink written 3.7 years ago by osa.zuta40
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 355 users visited in the last hour