I am trying to create a distance matrix for both Seurat and monocle object for clustering analysis of single cell RNA data analysis. Though I am following the tutorial in their respective websites, i am unable to retrieve distance matrix in any way.
Below is code for Monocle:
HSMM<- newCellDataSet(data, phenoData = pd, featureData = fd, lowerDetectionLimit = 0.5, expressionFamily = negbinomial.size()) HSMM <- estimateSizeFactors(HSMM) HSMM <- estimateDispersions(HSMM) HSMM <- reduceDimension(HSMM, max_components = 2, num_dim = 6, reduction_method = 'tSNE', verbose = T) HSMM <- clusterCells(HSMM, num_clusters = 5)
pbmc1<- CreateSeuratObject(dat, min.cells = 3, project = "test",min.features = 200) pbmc1 <- subset(pbmc1, subset = nFeature_RNA > 200 & nFeature_RNA < 6000 & percent.mt < 5) pbmc1 <- NormalizeData(pbmc1) pbmc1 <- FindVariableFeatures(pbmc1, selection.method = "vst") pbmc1<- ScaleData(pbmc1, features = rownames(pbmc1)) pbmc1 <- RunPCA(pbmc2, features = VariableFeatures(pbmc2), ndims.print = 6:10, nfeatures.print = 10)
I would be obliged if any one helps me
Thanks in advance