Hi,
Please 'reply all' when responding so communication stays on the list.
If you are working with stranded ranges you should use the GRanges
container. IRanges is not strand-aware and does not have a strand
argument. You can see the function signature on the man page by typing
?IRanges
> Usage:
>
> ## IRanges constructor:
> IRanges(start=NULL, end=NULL, width=NULL, names=NULL)
>
Load a Transcript Db object and extract transcripts by gene:
library(TxDb.Dmelanogaster.UCSC.dm3.ensGene)
tx <- transcriptsBy(TxDb.Dmelanogaster.UCSC.dm3.ensGene, "gene")
Select a gene with transcripts on the negative strand:
gene <- tx[[3]]
>> gene
> GRanges with 4 ranges and 2 metadata columns:
> seqnames ranges strand | tx_id tx_name
> <rle> <iranges> <rle> | <integer> <character>
> [1] chr3R [12632936, 12655767] - | 21863 FBtr0306337
> [2] chr3R [12633349, 12653845] - | 21864 FBtr0083388
> [3] chr3R [12633349, 12655300] - | 21865 FBtr0083387
> [4] chr3R [12633349, 12655474] - | 21866 FBtr0300485
GRanges can be manipulated with resize(), trim(), shift(), flank(),
narrow() and several other methods. To see them type (with the quotes)
?`intra-range-methods`
and select the page for GRanges. It sounds like resize() is what
you're
looking for.
resize(gene, width = 10)
>> resize(gene, width = 10)
> GRanges with 4 ranges and 2 metadata columns:
> seqnames ranges strand | tx_id tx_name
> <rle> <iranges> <rle> | <integer> <character>
> [1] chr3R [12655758, 12655767] - | 21863 FBtr0306337
> [2] chr3R [12653836, 12653845] - | 21864 FBtr0083388
> [3] chr3R [12655291, 12655300] - | 21865 FBtr0083387
> [4] chr3R [12655465, 12655474] - | 21866 FBtr0300485
If you have sequence data instead of range data, the XStringSet family
is more appropriate. For examples of manipulating sequences see
Section
E on the XStringSet man page. The functions you want are narrow() or
subseq().
library(Biostrings)
?XStringSet
Valerie
On 08/08/2014 08:38 AM, carol white wrote:
> I have the problem when i want to take the width from the end of a
> sequence on a reverse strand.
> if I take the nucleotide seq of a gene that is on the reverse strand
on
> the ncbi web site and extract for ex 10 or 20 bp from the end, i
don't
> get the same as I do with iranges. As I have already given the
strand as
> the parameter to the iranges function, I assume that it has already
> reverse-complemented by iranges. I don't have this problem with the
> genes that are on the forward strand nor when I take the sub
sequence
> from the beginning of the sequence.
>
> Regards,
> On Friday, August 8, 2014 5:28 PM, Valerie Obenchain
> <vobencha at="" fhcrc.org=""> wrote:
>
>
> Did you provide 'start', 'end' and 'width' and get a confusing
answer?
> If yes, please show your example.
>
> Thanks.
> Valerie
>
>
>
> On 08/08/2014 08:23 AM, Valerie Obenchain wrote:
> > Hi Carol,
> >
> > The 'end' is the end of the range. When you specify ranges with
'end'
> > and 'width' the range will always end at the 'end' value.
> >
> > > IRanges(end = 10, width = c(5, 10))
> > IRanges of length 2
> > start end width
> > [1] 6 10 5
> > [2] 1 10 10
> >
> >
> > Similar reasoning for 'start' and 'width':
> >
> > > IRanges(start = 10, width = c(5, 10))
> > IRanges of length 2
> > start end width
> > [1] 10 14 5
> > [2] 10 19 10
> >
> >
> > Valerie
> >
> >
> >
> > On 08/08/2014 01:29 AM, carol white wrote:
> >> Hi,
> >> How does width with start and end in IRanges work? I thought
that if I
> >> use the end with a width, then the sequence from the end with
the
> >> length of width is taken. However, in my case when I use width
for ex
> >> 20 and 10, the corresponding sequences with the length 20 and 10
are
> >> not the same from the end but from the beginning. Did I
misunderstood
> >> some thing?
> >>
> >> Regards,
> >>
> >> Carol
> >> [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org="">
> >>
https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
> >>
http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >
> >
>
>
> --
> Valerie Obenchain
> Program in Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, Seattle, WA 98109
>
> Email: vobencha at fhcrc.org <mailto:vobencha at="" fhcrc.org="">
> Phone: (206) 667-3158
>
>
