I want to make a html report with Rmarkdown of an OUTRIDER script. But I get an error when it comes to calculation q (function: findEncodingDims() and plot in with plotEncDimSearch(q)) This function does work when I run only that part of the script in R.

```{r filter, echo=FALSE}
ods <- filterExpression(ods, minCounts=TRUE, filterGenes=TRUE)
```

```{r q, echo=FALSE}
ods <- estimateSizeFactors(ods)

# calculate optimal q (default zScore = 3)
q <- findEncodingDim(ods, params = seq(2, min(100, ncol(ods) -1, nrow(ods) -1), 2), zScore = 3)
plotEncDimSearch(q)
# best optimum is 2
ods <- controlForConfounders(ods, q = 2, iterations=15)
```


Error in `:=`(opt, encodingDimension[which.max(evalutionLoss)[1]]) : Check that is.data.table(DT) == TRUE. Otherwise, `:=` (...) are defined for use in j, once only and in paricular ways. See help (":="). Calls: <Anonymous> ... withVisible -> eval -> eval -> plotEncDimSearch -> := Execution halted

Is this a known problem, or what can I do to solve this?

Best regards,

Monique van Veghel

https://www.dropbox.com/s/89wi9wy8kn0puyq/Schermafdruk%202020-05-15%2013.01.24.png?dl=0