New vignette hangs with reduced dataset about discbio

[wleoncio]

So think I got the answer from a script attached to an e-mail. Using sc <- Clustexp(sc, cln=2) and 2 clusters from then on works. As a matter of fact, that whole script works for the vignette (with minor adjustments), so I'll use it as a base for the document.

[SystemsBiologist]

Here we go:

DataSet <- valuesG1msReduced
sc <- DISCBIO(DataSet)
sc<-NoiseFiltering(sc,percentile=0.9, CV=0.2)

Normalizing the reads without any further gene filtering

sc<-Normalizedata(sc, mintotal=1000, minexpr=0, minnumber=0, maxexpr=Inf, downsample=FALSE, dsn=1, rseed=17000)

sc<-FinalPreprocessing(sc,GeneFlitering="NoiseF",export = TRUE)
sc<- Clustexp(sc,cln=2,quiet=TRUE) #### K-means clustering to get three clusters

cdiff <- DEGanalysis(
sc, Clustering="K-means", K=2, fdr=0.1, name="Name", export=TRUE,
quiet=FALSE
)