AnnotationForge::makeOrgPackage "argument is missing, with no default" Errors
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Entering edit mode
Mistinrain ▴ 10
@d97f3ccd
Last seen 16 months ago
United States

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 <liuchangbio@163.com>',
+   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 <liuchangbio@163.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!

AnnotationForge • 588 views
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1
Entering edit mode
Mistinrain ▴ 10
@d97f3ccd
Last seen 16 months ago
United States

I think I know the reason for the error, it was caused by an extra comma in the last line, and after deleting it, the problem was solved! Yeah!

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