在利用monocle2对seurat数据进行拟时序分析,在创建newCellDataSet时出现以下报错,
Error in validObject(.Object) : 类别为“CellDataSet”的对象不对: sampleNames differ between assayData and phenoData
按照monocle2的说明书featureData,phenoData分别由以下代码获得,
phenoData:
monocle.matrix <- as.matrix(scRNA_sub@assays$RNA@data)
monocle.sample <- scRNA_sub@meta.data
pd<-new("AnnotatedDataFrame", data = monocle.sample)
phenoData = pd
featureData:
monocle.geneAnn <- data.frame(gene_short_name = row.names(monocle.matrix), row.names = row.names(monocle.matrix))
fd<-new("AnnotatedDataFrame", data = monocle.geneAnn)
featureData = fd
创建newCellDataSet时的代码如下:
data <- as(as.matrix(monocle.matrix), 'sparseMatrix')
cds <- newCellDataSet(data, phenoData = pd, featureData = fd)
新人求教,还请大佬们不吝赐教