I am using Monocle to construct pseudotime trajectories on some skin data. Everything has run and it is working fine. Going over my script, I can still see some parameters I have set which I just used from the Monocle tutorial. Looking into them a bit more, I have two main queries:
1.) When I use the detectGenes function at the beginning of my script to filter for genes above a specific threshold value, it is not clear in the documentation where the min_exp values I decide to set are being compared to.
detectGenes(monocleobject, minexpr = 0.1)
I assume it is referring to this table in the Monocle object (monocle_object@assaydata$exprs) but I am unsure.
2.) Before performing a differential gene test across clusters to identify genes which define progression across pseudotime, I use this line from the tutorial to filter for genes present in >x nr cells:
monocleobjectexpressedgenes <- row.names(subset(fData(monocleobject), numcellsexpressed >= 10))
I am unsure how the numcellsexpressed values are computed by Monocle. I know they are taken from the phenodata in the Monocle object but does this just include genes with non-zero values for expression or is it above a threshold? This is not so clear.
Does anyone have any advice on this so I better set these filters?