monocle error at orderCells
Entering edit mode
444579004 • 0
Last seen 23 months ago

hi! I use monocle to make a pseudotime anlysis with my single cell sequencing data. After dimension reduction and cluster, when I try to order cells using the function "orderCells",the error occurred. The error is: "Error in graph.adjacency.dense(adjmatrix, mode = mode, weighted = weighted, : long vectors not supported yet: ../../src/include/Rinlinedfuns.h:519"

The code i use is showed below: library(dplyr) library(Seurat) library(monocle) library(Biobase) library(knitr) library(reshape2) library(ggplot2) library(HSMMSingleCell) library( t <- readRDS(file = "/home/zhangs/t20190829.rds")

import our data as a celldataset

the matrix including data of genes and cells

matrix <- as.matrix(t@data)

the data of cells

pd <- new('AnnotatedDataFrame', data =

the data of genes

fdata <- data.frame(geneshortname = row.names(matrix), row.names = row.names(matrix)) fd <- new('AnnotatedDataFrame', data = fdata)

whole dataset

monocle <- newCellDataSet(matrix, phenoData = pd, featureData = fd, expressionFamily=negbinomial.size())

this row is to decide the distribution of data

look at the cell data and change the name of upstream cluster information

head(pData(monocle)) names(pData(monocle))[names(pData(monocle)) == "res.1"] = "seucluster"

this step will help us with differentied gene expression

monocle <- estimateSizeFactors(monocle) monocle <- estimateDispersions(monocle) monocle <- detectGenes(monocle, minexpr = 0.1) expressedgenes <- row.names(subset(fData(monocle), numcellsexpressed >= 10))

disptable <- dispersionTable(monocle) orderinggenes <- subset(disptable, meanexpression >= 0.5 & dispersionempirical >= 1 * dispersionfit)$geneid monocle <- setOrderingFilter(monocle, orderinggenes) plotorderinggenes(monocle) plotpcvarianceexplained(monocle, returnall = F) monocle <- reduceDimension(monocle, maxcomponents = 2, numdim = 10, reductionmethod = 'tSNE', verbose = T) monocle <- clusterCells(monocle) plotcellclusters(monocle, 1, 2, colorby= "Cluster", showcellnames = T, cellsize = 0.5) difftestres <- differentialGeneTest(monocle[expressedgenes,], fullModelFormulaStr="~Cluster") monocleorderinggenes <- row.names(difftestres)[order(difftestres$qval)][1:1000]

monocle <- setOrderingFilter(monocle, orderinggenes = monocleordering_genes)

monocle <- reduceDimension(monocle, method = 'DDRTree')

monocle <- orderCells(monocle)

plotcelltrajectory(monocle, color_by = "Hours")

monocle <- setOrderingFilter(monocle, unsupclusteringgenes$geneid) orderinggenes <- row.names (subset(difftestres, qval < 0.01)) monocle <- setOrderingFilter(monocle, orderinggenes) plotordering_genes(monocle)

monocle <- reduceDimension(monocle, maxcomponents=2) monocle <- orderCells(monocle) colnames(pData(monocle)) plotcelltrajectory(monocle, colorby="Cluster")

I have never met this error before,can anyone used to this packages tell me what it means and how can i fix it?

scRNA monocle packages Tutorial • 870 views
Entering edit mode

It looks from the developer's website that the Bioconductor version of Monocle (aka Monocle 2) is deprecated, and you should move to the newer version Monocle 3:


Login before adding your answer.

Traffic: 445 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6