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tilschaef / scRNA-seq

From fastq to preprocessed counttable (for in-house CELSeq2 method), with Kallisto | Bustools workflow.
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JackStraw settings hardcoded #11

Closed Rebecza closed 3 years ago

Rebecza commented 3 years ago

Considering: JackStraw can be used to run for checking significant PCs, however the settings were hardcoded for the amount of dims.

This is an issue in larger datasets where the variability is contained in more than the first 20 PCs.

Within the following chunks, I tried changing the hardcoded amounts of dims, and this should work with the following code (I checked only with 30):

Perform JackStraw Permutations to find significant PCs

seuset.jack <- JackStraw(
   object = seuset,
   dims = 30,
   num.replicate = 100
)
seuset.jack <- ScoreJackStraw(seuset.jack, dims = 1:30)
JackStrawPlot(object = seuset.jack, dims = 1:30)

So we could add a jackstraw_pc variable? Or maybe this works with the PC amount set for params$pcs_max_hvg