Question

How do I get groseq signal for each gene from groSeq in groHMM

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@jsalsager-14698

Last seen 11 months ago

United States

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 • 1.2k views

ADD COMMENT • link updated 6.1 years ago by anusha.nagari ▴ 50 • written 6.1 years ago by Deleted ▴ 70

score 3 · Answer 1 · 2018-10-02

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anusha.nagari ▴ 50

@anushanagari-8496

Last seen 2.5 years 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)

ADD COMMENT • link 6.1 years ago anusha.nagari ▴ 50

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Thank you again, I really appreciate your help!

ADD REPLY • link 6.1 years ago Deleted ▴ 70

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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)

ADD REPLY • link 6.1 years ago Deleted ▴ 70