Question

SGSeq: moving toward diffex from SGSeq analysis

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Sylvain Foisy ▴ 70

@sylvain-foisy-5539

Last seen 4.6 years ago

Canada

Hi,

I have use SGSeq mostly to look at exon usage for genes of interest in my RNASeq datasets. I would like to move toward exon diffex analysis. I followed the recipes in the HTML guide to get counts, exons and gene ID but I am perplexed about what I got... I have an SGFeatureCounts object with created from rowRanges on the SGVariantCounts object previously created that has all the infos like geneName, etc. However, after performing the getSGVariantCounts method on it and using the eventID method, I only get integers, that I am guessing are the positions of the genes in the previous object. How can I get geneName instead or possibly add geneName data on the objects?

I am guessing that it would always be possible to go back with integer values to explore the SGFeatureCounts object?

Thanks in advance

S

sgseq rnaseq • 1.6k views

ADD COMMENT • link updated 6.7 years ago by Leonard Goldstein ▴ 170 • written 6.7 years ago by Sylvain Foisy ▴ 70

score 2 · Answer 1 · 2017-08-23

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Leonard Goldstein ▴ 170

@leonard-goldstein-6845

Last seen 14 months ago

Australia

Hi Sylvain,

Not sure I completely follow your question. You seem to be confusing SGFeatureCounts and SGVariantCounts objects. The idea behind section 11 of the vignette is to test for differential splice variant usage within a splice event, rather than differential exon usage within a gene. This approach will detect differential splice events (which are identified by event IDs) and you can look them up in your original SGVariants/Counts object.

Leonard

ADD COMMENT • link 6.7 years ago Leonard Goldstein ▴ 170

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Hi Leonard,

No problem ;-) Ok, as per section 11, I created objects for counts, exon ID and gene ID with the methods in the vignette:

# My R stuff:
# sgfc.denovo.var is my equivalent to sgvc_pred
> sgv.ranges<-rowRanges(sgfc.denovo.var)
> sgv.counts<-getSGVariantCounts(sgv.ranges,sample_info=data.r)
> x <-counts(sgv.counts)
> vid<-variantID(sgv.counts> 
> eid<-eventID(sgv.counts)

When I look at vid or eid, I only get matrices of integer values, so I am guessing that they are corresponding indexes in the previous sgv.ranges object. Am I right? If this is the case, what is the easiest way to make out the gene symbol from the geneName column in sgv.ranges?

Thanks in advance

S

ADD REPLY • link 6.7 years ago Sylvain Foisy ▴ 70

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Hi Sylvain,

Yes variantID() and eventID() are accessor functions for metadata columns in the SGVariant/Counts objects. You can see all available columns by typing mcols(sgv.counts). To extract gene names you can simply use geneNames(sgv.counts). Note this will return an empty CharacterList unless you previously annotated your predictions. I hope this helps.

Leonard

ADD REPLY • link 6.6 years ago Leonard Goldstein ▴ 170

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Hi Leonard,

Thanks for the info; I'll be playing some more and if needed, may be bug you again ;-)

Best regards

S

ADD REPLY • link 6.6 years ago Sylvain Foisy ▴ 70