Good morning,
I have a question about number of features. Since I have a lot number of features, I want to reduce number of features in my seurat object. I am wondering can I reduce the number of features?
dim(panc8_sub)
[1] 34368 851927
This is the code I use for quality control:
for (i in 1:length(scRNAlist)) { scRNAlist[[i]] <- NormalizeData(scRNAlist[[i]], verbose = FALSE) scRNAlist[[i]] <- FindVariableFeatures(scRNAlist[[i]], selection.method = "vst", nfeatures = 2000, verbose = FALSE) scRNAlist[[i]][["percent.mt"]] <- PercentageFeatureSet(object = scRNAlist[[i]], pattern = "^MT-") ##mito genes
Feature_range = quantile(scRNAlist[[i]]$nFeature_RNA, probs=c(.025,.975)) Count_range = quantile(scRNAlist[[i]]$nCount_RNA, probs=c(.025,.975)) percent.mt_range = quantile(scRNAlist[[i]]$percent.mt, probs=c(.05, .975))
We filter cells that have unique feature counts over 2,500 or less than 200, cells that have >5% mitochondrial counts
scRNAlist[[i]] <- subset(scRNAlist[[i]], subset = nFeature_RNA > Feature_range[1] & nFeature_RNA < Feature_range[2] & percent.mt < 10 & nCount_RNA > Count_range[1] & nCount_RNA < Count_range[2]) scRNAlist[[i]]<- SCTransform(object = scRNAlist[[i]], vars.to.regress = "percent.mt", verbose = FALSE) }
