RnBeads - test statistics for rnb.run.differential
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Brian Smith ▴ 120
@brian-smith-6197
Last seen 2.0 years ago
United States

Hi,

I was running rnb.run.differential with the following code:

================

rnb.options("covariate.adjustment.columns"=c("AGE"))

rnb.options(export.to.ewasher=TRUE)
rnb.options(inference=TRUE)
rnb.options(differential.site.test.method="refFreeEWAS")
rnb.options("differential.comparison.columns"="Class")


rnb.run.differential(rnb.set=rnb.set4, dir.reports=report.dir4)

====================

 

I get the p.values in the results, but is there a way to get the underlying test statistic results as well (t-statistic/wald etc.)

thanks!

RnBeads • 1.1k views
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Entering edit mode
rnbeads • 0
@rnbeads-7880
Last seen 21 months ago
Germany

Hi,
yes, in. The "rnb.run.differential" function returns a result, that contains an object of type RnBDiffmeth in a slot named "diffmeth".
A function applicable to that object is called "get.site.test.method()" and should return what you are asking for:
dm <- rnb.run.differential(...)$diffmeth
get.site.test.method(dm)

HTH,
Fabian

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