Hello R gurus,

I used R "biomaRt" package to extract some annotation information about TNF
gene,

the code I used is as below:

-------------
library(biomaRt)
usemaRt(biomart="ensembl",dataset="hsapiens_gene_ensembl")->en
listAttributes(mart=en,category="Structures")$name->attributes
getBM(attributes=attributes, filters="entrezgene",values=7124,
mart=en)->temp
----------------

but the column names of the returned data frame is in confusion, head
information of the temp object is:
---
 struct_biotype cdna_length cds_length str_chrom_name constitutive
exon_cds_end exon_cds_start exon_chrom_end exon_chrom_start
exon_coding_end exon_coding_start rank exon_stable_id external_db_name
struct_external_gene_id gene_chrom_end gene_chrom_start gene_stable_id
peptide_length transcript_chrom_end transcript_chrom_start
transcript_chrom_strand transcript_count transcript_stable_id
translation_stable_id
1 protein_coding 1669 702 c6_COX 1 186 1 31678370 31678016 31678370
31678185 1 ENSE00001495979 Uniprot/SWISSPROT TNFA_HUMAN 31680778
31678016 ENSG00000206328 233 31680778 31678016 1 ENST00000383302
ENSP00000372790 1
2 protein_coding 1669 702 c6_COX 1 232 187 31679022 31678977 31679022
31678977 2 ENSE00001495978 Uniprot/SWISSPROT TNFA_HUMAN 31680778
31678016 ENSG00000206328 233 31680778 31678016 1 ENST00000383302
ENSP00000372790 1
3 protein_coding 1669 702 c6_COX 1 280 233 31679257 31679210 31679257
31679210 3 ENSE00001495976 Uniprot/SWISSPROT TNFA_HUMAN 31680778
31678016 ENSG00000206328 233 31680778 31678016 1 ENST00000383302
ENSP00000372790 1
4 protein_coding 1669 702 c6_COX 1 702 281 31680778 31679559 31679980
31679559 4 ENSE00001495975 Uniprot/SWISSPROT TNFA_HUMAN 31680778
31678016 ENSG00000206328 233 31680778 31678016 1 ENST00000383302
ENSP00000372790 1
5 protein_coding 1685 702 6 1 186 1 31651683 31651314 31651683
31651498 1 ENSE00001469490 HUGO TNF 31654092 31651314 ENSG00000204490
233 31654092 31651314 1 ENST00000376122 ENSP00000365290 1
6 protein_coding 1685 702 6 1 232 187 31652335 31652290 31652335
31652290 2 ENSE00001469486 HUGO TNF 31654092 31651314 ENSG00000204490
233 31654092 31651314 1 ENST00000376122 ENSP00000365290 1
---

obviously, the last column is wrong.

I think the problem happens when giving cloumn names for the retrieved
data.frame,
the order of the retrieved data.frame is not exactly the order of the
attributes.

what happened?

Any suggestions or helps would be greatly appreciated!


LiGang


-----
My platform:

platform       i386-pc-mingw32
arch           i386
os             mingw32
system         i386, mingw32
status
major          2
minor          6.0
year           2007
month          10
day            03
svn rev        43063
language       R
version.string R version 2.6.0 (2007-10-03)

LC_COLLATE=Chinese_People's Republic of China.936;
LC_CTYPE=Chinese_People's Republic of China.936;
LC_MONETARY=Chinese_People's Republic of China.936;
LC_NUMERIC=C;
LC_TIME=Chinese_People's Republic of China.936
---------------

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