Hi,
I'm stuck on loading my customize annotation on topgo using R. I have a .txt file containing list of genes and their GO Ids.
Genes Gene ontology IDs
c10020_g1 GO:0047021; GO:0019369; GO:0004090; GO:0019371; GO:0005829; GO:0017144; GO:0030855; GO:0070062; GO:0055114; GO:0016655; GO:0050221; GO:0044281; GO:0042373
c10035_g1 GO:0005524; GO:0016887; GO:0005929; GO:0005737; GO:0030286; GO:0005874; GO:0003777; GO:0007018; GO:0005515
c10052_g1 GO:0005737; GO:0016021; GO:0008168
When I tried to upload this to topgo, here's the error message:
> geneID2GO <- readMappings(file = ".../Htub_gene_list_complete_annots.txt", sep="\t")
Error in `[.data.frame`(a, , 2) : undefined columns selected
In addition: Warning messages:
1: In read.table(file = file, header = header, sep = sep, quote = quote, :
line 1 appears to contain embedded nulls
2: In read.table(file = file, header = header, sep = sep, quote = quote, :
line 3 appears to contain embedded nulls
3: In read.table(file = file, header = header, sep = sep, quote = quote, :
line 4 appears to contain embedded nulls
4: In read.table(file = file, header = header, sep = sep, quote = quote, :
line 5 appears to contain embedded nulls
5: In scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
embedded nul(s) found in input
I can't figure out what is wrong? Can somebody help me. thanks!
Best,
Christine
I'm stuck on loading my customize annotation on topgo using R. I have a .txt file containing list of genes and their GO Ids.
Genes Gene ontology IDs
c10020_g1 GO:0047021; GO:0019369; GO:0004090; GO:0019371; GO:0005829; GO:0017144; GO:0030855; GO:0070062; GO:0055114; GO:0016655; GO:0050221; GO:0044281; GO:0042373
c10035_g1 GO:0005524; GO:0016887; GO:0005929; GO:0005737; GO:0030286; GO:0005874; GO:0003777; GO:0007018; GO:0005515
c10052_g1 GO:0005737; GO:0016021; GO:0008168
When I tried to upload this to topgo, here's the error message:
> geneID2GO <- readMappings(file = ".../Htub_gene_list_complete_annots.txt", sep="\t")
Error in `[.data.frame`(a, , 2) : undefined columns selected
In addition: Warning messages:
1: In read.table(file = file, header = header, sep = sep, quote = quote, :
line 1 appears to contain embedded nulls
2: In read.table(file = file, header = header, sep = sep, quote = quote, :
line 3 appears to contain embedded nulls
3: In read.table(file = file, header = header, sep = sep, quote = quote, :
line 4 appears to contain embedded nulls
4: In read.table(file = file, header = header, sep = sep, quote = quote, :
line 5 appears to contain embedded nulls
5: In scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
embedded nul(s) found in input
I can't figure out what is wrong? Can somebody help me. thanks!
Best,
Christine
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