Extracting Statistically Significant Differentially Expressed Exons From Dexseq Results
2
0
Entering edit mode
8.2 years ago
pm2013 ▴ 50

Hi

I am trying to extract some data from my DEXseq results. I was able to get the final HTML report for my analysis. However, I was wondering if there's a way I could extract specific exons that are significantly differentially expressed between two conditions. I am interested in getting the gene id (ensembl gene id ok), exon or exon bin id (if applicable), their exon boundaries, fold change & adjusted p value. I am a R/bioconductor newbie. Any help is appreciated.

Thanks

rna-seq bioconductor r splicing • 3.9k views
ADD COMMENT
1
Entering edit mode
8.2 years ago

In part, you can get that from res <- DEUresultTable(ecs), where ecs is an ExonCountSet. The coordinates are in featureData(ecs). You can then get the log2 foldchange with estimatelog2FoldChanges(ecs, ...)

ADD COMMENT
0
Entering edit mode

Thank you for your comment. I will try your suggestions. Looks like there's no straightforward way to this.

ADD REPLY
0
Entering edit mode
6.6 years ago
Fahmi • 0

Hello, how could I get the statistically significant for DEXSeq result. The output which I got from html only the sorted result based on Ensembl name without the p-value or q-value. How do I get that result? Thank you

ADD COMMENT
0
Entering edit mode

Get the non-HTML results. If you didn't do the analysis yourself then ask whomever did do it for a csv file or something like that.

ADD REPLY
0
Entering edit mode

Is it from the dxr result? Do you mind to show me the code for this. I tried before didn't get it.

ADD REPLY
0
Entering edit mode

Assuming "dxr" is the output of DEXSeqResults() then yes, that's a table with everything in it. Just write it to a file.

ADD REPLY

Login before adding your answer.

Traffic: 1741 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6