I try to simulate multiple(30) cell type from a real scRNA data and set the parameter 'group' to the cell type vector. The reference data was normalized by 'NormalizeData' in 'Seurat' package.(normalization.method = 'LogNormalize')
But, in the end, the simulation data is divided into 2 parts in the UMAP and not group by cell type.
The parameter:
result = SPsimSeq(n.sim = 1, s.data = ref, group = ref$re_refcell, n.genes = 10000, group.config = re
p(1/30, 30), pDE = 0.1, lfc.thrld = 0.25, tot.samples = 3000, model.zero.prob = TRUE, genewiseCor = T
RUE, result.format = "SCE", log.CPM.transform = FALSE)
I try to simulate multiple(30) cell type from a real scRNA data and set the parameter 'group' to the cell type vector. The reference data was normalized by 'NormalizeData' in 'Seurat' package.(normalization.method = 'LogNormalize')
But, in the end, the simulation data is divided into 2 parts in the UMAP and not group by cell type.
The parameter:
result = SPsimSeq(n.sim = 1, s.data = ref, group = ref$re_refcell, n.genes = 10000, group.config = re
p(1/30, 30), pDE = 0.1, lfc.thrld = 0.25, tot.samples = 3000, model.zero.prob = TRUE, genewiseCor = T
RUE, result.format = "SCE", log.CPM.transform = FALSE)