[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
>



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