Question: What assays are distributed with Recount TX data
0
gravatar for k.vitting.seerup
9 months ago by
European Union
k.vitting.seerup90 wrote:

When downloading Recount2 tx-dataset (either via the R package or via their website) such as this dataset I get a RangedSummarizedExperiment which contain 4 assays:

assays(rse_tx)

  • "fragments"
  • "ses"
  • "scores"
  • "df"

Fragments are self-explanatory (counts from paired end data) - but what are the other 3 "assays".

In advance - thanks!

ADD COMMENTlink written 9 months ago by k.vitting.seerup90
1

Hi there, "ses" is the standard errors of the fragments estimates, "scores" is score between 0 and 1 that dictates how uniquely identifiable each transcript is under the model we fit (0 being perfectly redundant, and 1 being perfectly unique). "df" is the degrees of freedom that particular transcript has in the linear model. Thanks!

 

 

ADD REPLYlink written 9 months ago by jmfu10

Thanks! You should have added that as an answer so I could mak it as solved :-)

ADD REPLYlink written 9 months ago by k.vitting.seerup90

Yup, please do so Jack! ^^ This info gets reflected at the top of the package page http://bioconductor.org/packages/release/bioc/html/recount.html

 

Thanks!

ADD REPLYlink written 9 months ago by Leonardo Collado Torres650
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