[BioC] "start" filter in biomaRt
Shi, Tao
shidaxia at yahoo.com
Mon Aug 25 20:15:23 CEST 2008
Hi list,
In the following code, I'm using 'biomaRt' to retrieve all the genes that start beyond 1000000 on chromosome 17. However, I'm not expecting the first gene which starts at 853510 to be in the resulting list. It seems the "start" filter is not just simple ">=". More explanations, please!
Thanks!
...Tao
> library(biomaRt)
Loading required package: RCurl
> mart = useMart("ensembl", dataset="hsapiens_gene_ensembl")
Checking attributes and filters ... ok
> tmp2 <- getBM(attributes=c("ensembl_gene_id","start_position","end_position"),filters = c("chromosome_name", "start"), values=list("17", "1000000"), mart = mart)
> tmp2[order(tmp2$start_position),][1:10,]
ensembl_gene_id start_position end_position
1135 ENSG00000159842 853510 1029881
1442 ENSG00000205899 1120603 1121504
690 ENSG00000184811 1129707 1151031
1134 ENSG00000209456 1156460 1156529
452 ENSG00000108953 1194595 1250267
451 ENSG00000167193 1272190 1306294
1133 ENSG00000197879 1314232 1342633
450 ENSG00000132376 1344622 1366719
689 ENSG00000174238 1368037 1412835
449 ENSG00000167703 1424448 1478880
> sessionInfo()
R version 2.7.0 (2008-04-22)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_1.14.0 RCurl_0.9-3
loaded via a namespace (and not attached):
[1] XML_1.95-2
>
More information about the Bioconductor
mailing list