How do I use SCTransform+harmony integrated dataset for scclusteval cluster evaluation

Open Paria06 opened this issue 3 years ago • 1 comments

Hi @crazyhottommy I would like to make sure I made the changes correctly as I'm doing SCT and Harmony. The changes Made are as below: L52 (RunPCA > RunHarmony): set.seed(1) object<- RunHarmony(object = object, assay.use="SCT", group.by.vars = "orig.ident")

L76-77 (pca > harmony): object<- FindNeighbors(object, dims = 1:pc.use, k.param = k.param, nn.eps = nn.eps, verbose = FALSE, reduction = "harmony", force.recalc = TRUE)

Moreover, does it matter How I do the steps and what I regress out? below is my code for SCT and harmony: code:

I have one more question; do I need to edit the preprocess.R script as it specified the pc.use=20 and in the downstream analysis it stops if the code asks for more than 20 PCs.

Thank you in advance!

Aug 02 '22 15:08 Paria06

The code looks okay to me.

and yes, for pc.use https://github.com/crazyhottommy/pyflow_seurat_parameter/blob/master/scripts/preprocess.R#L29

Aug 31 '22 11:08 crazyhottommy