Distance matrix for monocle and seurat object

Question

[rprog008]

Dear members,

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)

and seurat

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

[jared.andrews07]

Both methods have their own clustering functions. You're using Monocle's function, but Seurat's is FindClusters. Additionally, it's not clear what your actual issue is. Are you getting error messages?

[rprog008]

I apologize, if my question is unclear.

I am trying to retrieve the distance matrix from both seurat and monocle object in matrix form.

For instance in case of monocle, if I am writing

cellPairwiseDistances(HSMM)

or

HSMm@cellPairwiseDistances

I am getting 0x0 matrix.

However, clustering has been performed successfully.

Answer 1

[abbie.ireland]

Hello,

I am having this same issue with 0x0 matrix with my cds. Despite successful clustering, I can't get cellPairwiseDistance(cds) or reducedDimS(cds) to output anything but 0x0 matrices. Were you ever able to resolve?