How do I get groseq signal for each gene from groSeq in groHMM
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jsalsager ▴ 70
@jsalsager-14698
Last seen 2.3 years ago

hello!

I worked my way through the tutorial for groHMM but I'm not sure how to get signal (RPKM, FPKM etc.) for each gene.  The tutorial just shows how to make graphs.

Thanks!

groSeq groHMM • 627 views
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@anushanagari-8496
Last seen 6 months ago
UT SOUTHWESTERN MEDICAL CENTER

Hello,

You can do that using the following extension to section 3.8 in the tutorial:

d <- calcNormFactors(d)
d_rpkm <- data.frame(rpkm(d,width(kgChr7),normalized.lib.sizes=TRUE))
gene_rpkm <- data.frame(kgChr7,kgLimit, d_rpkm)
head(gene_rpkm)

 

 

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Thank you again, I really appreciate your help!

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Can I bug you with one final question?

If I wanted to export a similar file but using groHMM called transcripts rather than knownGenes, how would I change that code? I tried switching kgLimit with txLimit and ended up getting errors that I was combining a date.frame with different lengths.

Thanks so much for all your help!

Edit:

Would this work?

d_rpkm <- data.frame(rpkm(d,width(txFinal),normalized.lib.sizes=TRUE))
transcript_rpkm <- data.frame(txFinal, d_rpkm)
head(transcript_rpkm)
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