[BioC] converting position from '-' strand to '+' strand

[michael watson (IAH-C)]

Begin from the 5' end of what? Chromosomes don't have a 5' "end" 
________________________________________
From: bioconductor-bounces at stat.math.ethz.ch [bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Tim Smith [tim_smith_666 at yahoo.com]
Sent: 05 April 2010 20:07
To: bioc
Subject: [BioC] converting position from '-' strand to '+' strand

Apologies if this seems like a trivial question.

I wanted to have a consistent set of locations and wanted to all the locations to begin from the 5' end. How can I convert locations that are given for the '-' strand?
For example:
-----------------------------
library(biomaRt)

mart.obj <- useMart(biomart = 'ensembl', dataset = 'hsapiens_gene_ensembl')

atb <- c('ensembl_gene_id', 'chromosome_name', 'start_position', 'end_position', 'strand')

mir.locs <- getBM(attributes=atb, filters="biotype", values="miRNA", mart=mart.obj)
mir.locs[1:5,]
>  ensembl_gene_id chromosome_name start_position end_position strand
1 ENSG00000222732               5      171706206    171706319      1
2 ENSG00000207864               9       97847727     97847823      1
3 ENSG00000221173               9      129338809    129338909     -1
4 ENSG00000222961               5       32379501     32379581     -1
5 ENSG00000221058              18       51612956     51613026     -1


----------------------------
Is there a quick way that I can convert the last 3 rows so that they reflect positions from the 5' strand?
many thanks!



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