cell_trajectory_monocle3.r脚本使用报错

这是我的命令

Rscript $scripts/cell_trajectory_monocle3.r \

--rds ../06.subset/inflorescence.added.subtype.qs \

--use.seurat.umap --groupby subtype \

-o monocle3.inflorescence1 \

--root.cell inflorescence_primordia6 \

-k 5 --cpu 40 \

--gene2pathway ../ref/kegg.gene2pathway1.tsv \

--gene2go ../ref/go.go_anno_result1.tsv

这是报错，总是出现Column `group` is not found.，我的文件中没有这Column `group`

Error in `group_by()`:

! Must group by variables found in `.data`.

✖ Column `group` is not found.

Backtrace:

▆

1. ├─enrichGO %>% group_by(group) %>% slice_head(n = topn)

2. ├─dplyr::slice_head(., n = topn)

3. ├─dplyr::group_by(., group)

4. └─dplyr:::group_by.data.frame(., group)

5. └─dplyr::group_by_prepare(.data, ..., .add = .add, error_call = current_env())

6. └─rlang::abort(bullets, call = error_call)

Warning message:

the ‘subbars’ function has moved to the reformulas package. Please update your imports, or ask an upstream package maintainter to do so.

This warning is displayed once per session.

Execution halted

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默认排序时间排序

2 个回答

omicsgene - 生物信息 14小时前

擅长：重测序,遗传进化,转录组,GWAS

--gene2pathway ../ref/kegg.gene2pathway1.tsv \

--gene2go ../ref/go.go_anno_result1.tsv

你的上面这两个文件，看看文件格式是不是和课程里面的相同，并检查第一列信息的基因ID和你的单细胞里面的feature ID是不是一致：

$ head Gene_longest_trans_cds.fasta.GO.gsea.txt
GID	GO	DESC	CLASS
A1CF	GO:0000166	nucleotide binding	Molecular Function
A1CF	GO:0003727	single-stranded RNA binding	Molecular Function
A1CF	GO:0005654	nucleoplasm	Cellular Component
A1CF	GO:0005737	cytoplasm	Cellular Component
A1CF	GO:0010609	mRNA localization resulting in posttranscriptional	Biological Process
A1CF	GO:0016554	cytidine to uridine editing	Biological Process
A1CF	GO:0016556	mRNA modification	Biological Process
A1CF	GO:0030895	apolipoprotein B mRNA editing enzyme complex	Cellular Component
A4GALT	GO:0001576	globoside biosynthetic process	Biological Process

$ head Gene_longest_trans_cds.fasta.Kegg.gsea.txt
GID	Pathway	Pathway-Name
ACSS1	ko00010	Glycolysis / Gluconeogenesis
ACSS2	ko00010	Glycolysis / Gluconeogenesis
ADPGK	ko00010	Glycolysis / Gluconeogenesis
AKR1A1	ko00010	Glycolysis / Gluconeogenesis
ALDH1A3	ko00010	Glycolysis / Gluconeogenesis
ALDH2	ko00010	Glycolysis / Gluconeogenesis
ALDH7A1	ko00010	Glycolysis / Gluconeogenesis
ALDH8A1	ko00010	Glycolysis / Gluconeogenesis
ALDH9A1	ko00010	Glycolysis / Gluconeogenesis

gz_li 13小时前

格式检查过了，没有问题，检查第一列信息的基因ID和我的单细胞里面的geneID是一致。feature ID如何进行检查？我的数据是SCT标准化会有影响嘛？

cell_trajectory_monocle3.r脚本使用报错

2 个回答

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