Describe the bug
Hello, thanks a lot for the very useful tool. I am trying it for the first time and I am starting from the already analyzed Seurat object.
I am importing and transforming the gtf file for the annotation with:
tx2gene <- import_gtf(gtf_file = "Mus_musculus.GRCm39.109.gtf.gz")
tx2gene$gene_name <- one_to_one_mapping(name = tx2gene$gene_name, id = tx2gene$gene_id)
tx2gene$transcript_name <- one_to_one_mapping(name = tx2gene$transcript_name, id = tx2gene$transcript_id)
tx2gene <- move_columns_to_front(df = tx2gene, columns = c("transcript_name", "gene_name"))
Then I run:
cts<-seur_obj_sub@assays$RNA$counts
seur_obj_sub <- combine_to_matrix(tx_list = cts ,seurat_obj = seur_obj_sub, tx2gene = tx2gene)
**since I have a Seurat object what is the tx_list input I schould use?
Error:
Trying to infer cell extensions from Seurat object
Error in combine_to_matrix(tx_list = cts, seurat_obj = seur_obj_sub, tx2gene = tx2gene) :
Could not 1:1 map inferred seurat cellname extensions and tx file list.
Either provide explicit cell extensions or try subsetting the seurat object, if you do not want to provide tx information for all samples.
TobiTekath
commented
5 months ago
Describe the bug Hello, thanks a lot for the very useful tool. I am trying it for the first time and I am starting from the already analyzed Seurat object. I am importing and transforming the gtf file for the annotation with: tx2gene <- import_gtf(gtf_file = "Mus_musculus.GRCm39.109.gtf.gz") tx2gene$gene_name <- one_to_one_mapping(name = tx2gene$gene_name, id = tx2gene$gene_id) tx2gene$transcript_name <- one_to_one_mapping(name = tx2gene$transcript_name, id = tx2gene$transcript_id) tx2gene <- move_columns_to_front(df = tx2gene, columns = c("transcript_name", "gene_name"))
Then I run: cts<-seur_obj_sub@assays$RNA$counts
seur_obj_sub <- combine_to_matrix(tx_list = cts ,seurat_obj = seur_obj_sub, tx2gene = tx2gene) **since I have a Seurat object what is the tx_list input I schould use?
Error: Trying to infer cell extensions from Seurat object Error in combine_to_matrix(tx_list = cts, seurat_obj = seur_obj_sub, tx2gene = tx2gene) : Could not 1:1 map inferred seurat cellname extensions and tx file list. Either provide explicit cell extensions or try subsetting the seurat object, if you do not want to provide tx information for all samples.
Thank you in advance for yout time!