Entering edit mode
Mistinrain ▴ 10@d97f3ccd
Last seen 14 days ago
Hi, I'm trying to create a custom annotation for S.sureus and then run an enrichment analysis with clusterProfiler. However, I met an error when running AnnotationForge::makeorgPackage(), which returns the following error:
> AnnotationForge::makeOrgPackage( + gene_info = gene_info, + go = gene2go, + maintainer = 'Liu Chang <firstname.lastname@example.org>', + author = 'Liu Chang', + outputDir = getwd(), + tax_id = 703339, + genus = 'Staphylococcus', + species = 'aureus', + goTable = 'go', + version = '1.0', + ) Error in AnnotationForge::makeOrgPackage(gene_info = gene_info, go = gene2go, : argument is missing, with no default
My code is:
AnnotationForge::makeOrgPackage( gene_info = gene_info, go = gene2go, maintainer = 'Liu Chang <email@example.com>', author = 'Liu Chang', outputDir = getwd(), tax_id = 703339, genus = 'Staphylococcus', species = 'aureus', goTable = 'go', version = '1.0', )
Two input files:
> head(gene_info) # A tibble: 6 × 2 GID Gene_Name <chr> <chr> 1 NZ_CP051191.1_1 Phage Terminase 2 NZ_CP051191.1_2 Phage portal protein 3 NZ_CP051191.1_3 Belongs to the peptidase S14 family 4 NZ_CP051191.1_4 Phage capsid family 5 NZ_CP051191.1_7 Phage head-tail joining protein 6 NZ_CP051191.1_10 Phage tail tube protein
> head(gene2go) # A tibble: 6 × 3 GID GO EVIDENCE <chr> <chr> <chr> 1 NZ_CP051191.1_14 GO:0008150 IEA 2 NZ_CP051191.1_14 GO:0016032 IEA 3 NZ_CP051191.1_14 GO:0019058 IEA 4 NZ_CP051191.1_14 GO:0019068 IEA 5 NZ_CP051191.1_14 GO:0044403 IEA 6 NZ_CP051191.1_14 GO:0044419 IEA
I don't understand why this error occurs, because I think I have already provided all the necessary documents.
Thankyou for your attention!