Question

Errors in makeOrgPackage

1

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knishida ▴ 20

@knishida-8230

Last seen 4.2 years ago

United States

I'm trying to create a custom OrgDb for tomato.

First I tried to add Uniprot table to the OrgDb with

https://github.com/kozo2/org.Sl.eg.db/blob/master/tomatoMakeOrgPkg.R

but I had an error like

May I ask for any advice?

I checked this error on R 3.2.2 + Annotation Forge 1.12.0 on Windows 10 and Mac OS X El Capitan‎.

You can reproduce this error with the following commands.

git clone git://github.com/kozo2/org.Sl.eg.db
cd org.Sl.eg.db
R
> install.packages("splitstackshape")
> source("https://bioconductor.org/biocLite.R")
> biocLite("AnnotationForge")
> source("tomatoMakeOrgPkg.R")

annotation error • 1.2k views

ADD COMMENT • link updated 8.5 years ago by James W. MacDonald 65k • written 8.5 years ago by knishida ▴ 20

1

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It seems like the function is expecting a data.frame, but fUniprot is a data.table (from cSplit())?

ADD REPLY • link 8.5 years ago Martin Morgan 25k

0

Entering edit mode

Many thanks for your advise.

fUniprot was data.table as you indicated.

I replaced it to data.frame it works well now.

https://github.com/kozo2/org.Sl.eg.db/issues/1

ADD REPLY • link 8.5 years ago knishida ▴ 20

score 1 · Answer 1 · 2015-10-20

> fUniprot <- as.data.frame(fUniprot)
> library(AnnotationForge)
> #makeOrgPackage(gene_info = fSym, chromosome = fChr, go = fGO,
> # this does NOT work
> makeOrgPackage(gene_info = fSym, chromosome = fChr, go = fGO, uniprot = fUniprot,
+                version = "0.1",
+                maintainer = "Kozo Nishida <knishida@riken.jp>",
+                author = "Kozo Nishida <knishida@riken.jp>",
+                outputDir = ".",
+                tax_id = "4081",
+                genus = "Solanum",
+                species = "lycopersicum",
+                goTable = "go")
Populating genes table:
genes table filled
Populating gene_info table:
gene_info table filled
Populating chromosome table:
chromosome table filled
Populating go table:
go table filled
Populating uniprot table:
uniprot table filled
table metadata filled
Loading required package: GO.db

'select()' returned many:1 mapping between keys and columns
Dropping GO IDs that are too new for the current GO.db
Populating go table:
go table filled
'select()' returned many:1 mapping between keys and columns
Populating go_all table:
go_all table filled
Creating package in ./org.Slycopersicum.eg.db