makeOrgPackage 函数中 goTable 的报错问题

[ShuaiNIEgithub]

洲更师兄好，
我参照了你的流程和 makeOrgPackage 函数，构建了我的植物物种库，但是遇到了一个问题：
只有当 godf 里面只含有 'GID','GO' 和 'EVIDENCE'的时候才可以创建成功，我加上一列 Ontology 的时候，就报错了，代码和结果如下：
（非常感谢你的分享）

str(godf)
'data.frame': 47178 obs. of 4 variables:
$ GID : chr "Rhsim03G0081900" "Rhsim03G0171300" "Rhsim11G0054300" "Rhsim13G0074400" .
$ GO : chr "GO:0000015" "GO:0000015" "GO:0000015" "GO:0000015" ...
$ Ontology: chr "CC" "CC" "CC" "CC" ...
$ EVIDENCE: chr "A" "A" "A" "A" ...
makeOrgPackage(go=godf , version = "1", maintainer = "nieshuai <[email protected]>", author="nieshuai <[email protected]>", outputDir = "~/test", tax_id = "11111",# 查询网站https://www.ncbi.nlm.nih.gov/taxonomy genus = "tt", species = "tt" , goTable = "go" )
Populating genes table:
genes table filled
Populating go table:
go table filled
table metadata filled
Error in makeOrgDbFromDataFrames(data, tax_id, genus, species, dbFileName, :
'goTable' must have three columns called 'GID','GO' and 'EVIDENCE'
In addition: There were 16 warnings (use warnings() to see them)
#这里报错失败了

godf <- godf[,c(1,2,4)]
str(godf)
'data.frame': 47178 obs. of 3 variables:
$ GID : chr "Rhsim03G0081900" "Rhsim03G0171300" "Rhsim11G0054300" ...
$ GO : chr "GO:0000015" "GO:0000015" "GO:0000015" "GO:0000015" ...
$ EVIDENCE: chr "A" "A" "A" "A" ...
makeOrgPackage(go=godf , version = "1", maintainer = "nieshuai <[email protected]>", author="nieshuai <[email protected]>", outputDir = "~/test", tax_id = "11111",# 查询网站https://www.ncbi.nlm.nih.gov/taxonomy genus = "tt", species = "tt" , goTable = "go" )
然后就创建成功了。