Dear All,

I want to find the chromosome start and end positions in bp for a fragment
delineated by two cytobands (eg. 5q13.1-5q13.2) ( in large scale). I tried
getBM( ) in package 'biomaRt', but didn't find a right attribute to use. If
using "chromosome_location", then I will get many locations instead of just
'start' and 'end' positions (see below). Should I extract the 1st and last
positions from the resulted table, or any other ways to go using biomaRt, or
even ways without using biomaRt?

Many thanks!

> ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
>
res=getBM(attributes=c("chromosome_name","chromosome_location"),filters=c("chromosome_name","band_start",
"band_end"),values=list("5","q13.1", "q13.2"), mart=mart)

> dim(res)
[1] 12208     2
> res[1:10,]
   chromosome_name chromosome_location
1                5                  NA
2                5            72892696
3                5            72893102
4                5            72893367
5                5            72893406
6                5            72893742
7                5            72893755
8                5            72893834
9                5            72893947
10               5            72894391

> sessionInfo()
R version 2.7.1 (2008-06-23)
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_1.95-3
>

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