Open zhouliping718828 opened 4 days ago
mCT.keggCompare <- lapply(c('Epithelial', 'Neutrophil', 'Myeloid', 'NK', 'T', 'B', 'Fibroblast'), function(x){ select <- at.meta%>% subset(mCT == x) Idents(select) <- factor(select$group, levels = c('old', 'young'))
result <- FindAllMarkers(select, assay = "RNA", slot = "counts", min.pct = 0, min.cells.group = 0, logfc.threshold = 0, return.thresh = Inf, test.use = "wilcox") result <- result %>% subset(cluster == "old") %>% # subset(p_val<0.05 & p_val_adj<0.25 & avg_log2FC>0.25) %>% .[order(-.$avg_log2FC),] %>% transform(mCT = x) %>% dplyr::rename(c('kegg' = 'gene')) return(result) })
I allow this code to analyze my seurat object, the error is as follows, “ Error in .subscript.2ary(x, i, j, drop = drop): subscript out of bounds”please help me analyze the possible reasons
mCT.keggCompare <- lapply(c('Epithelial', 'Neutrophil', 'Myeloid', 'NK', 'T', 'B', 'Fibroblast'), function(x){ select <- at.meta%>% subset(mCT == x) Idents(select) <- factor(select$group, levels = c('old', 'young'))
I allow this code to analyze my seurat object, the error is as follows, “ Error in .subscript.2ary(x, i, j, drop = drop): subscript out of bounds”please help me analyze the possible reasons