[BioC] GRanges list and reduce function

[Asma rabe]

Hi Vincent, Martin,

Thank you very much for your kind explanation.

For Martin:

>For exons group by _gene_, it's possible that genes are annotated to
contain exons from different chromosomes

How genes can be annotated to contain exons from different many chromosomes?



Best Regards,
Asma


On Fri, Aug 15, 2014 at 11:56 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:

> On 08/15/2014 03:20 AM, Asma rabe wrote:
>
>> Hi ,
>>
>>
>> I need a Granges object with exons data for  few chromosomes, i got
>> Granges
>> list of transcripts and their exons as follows:
>>
>>
>> library("TxDb.Hsapiens.UCSC.hg19.knownGene")
>>
>> txdb<-TxDb.Hsapiens.UCSC.hg19.knownGene
>>
>> tx_Exons<-exonsBy(txdb)
>>
>>
>>
>> 1-How to use reduce on Granges list?how to get the unique exons only and
>> exclude redundant exons?
>>
>>
> I'm not sure what this means -- you've asked for exons grouped by
> transcript, and there are not 'extra' exons in each transcript. Did you
> want exonsBy(txdb, "gene") ?
>
> reduce(tx_Exons) reduces within each transcript (list element); I'm not
> sure what you'd really like to do?
>
>
>
>> 2-How to select exons of certain chromosomes only ex: chr10? i tried the
>> following but i wonder why i got  GRnages list with empty Grange lists??
>>
>
> if you want to select transcripts where all exons are in certain
> chromosomes, note that
>
>   seqnames(tx_Exonss) %in% "chr10"
>
> returns an RleList, and
>
>   all(seqnames(tx_Exons) %in% "chr10")
>
> asks element-wise whether all elements of each Rle are TRUE, returning a
> logical vector of the same length as tx_Exons. So
>
>   tx_Exons[all(seqnames(tx_Exons) %in% "chr10")]
>
> returns the transcripts with all exons on chr10. For exons group by
> _gene_, it's possible that genes are annotated to contain exons from
> different chromosomes
>
>  exByGn = exonsBy(txdb, "gene")
>> table(elementLengths(runLength(seqnames(exByGn))))
>>
>
>     1     2     3     4     5     6     7     8
> 23182    77     4     3    19    38    76    60
>
> and only exons in chr10, preserving grouping by gene and removing genes
> without any exons in chr10, are
>
>  chr10 <- exByGn[seqnames(exByGn) %in% "chr10"]
>>
>
> this is what you did below. The result is not empty, just contains the
> many transcripts with exons not in chr10 removed, plus those deep in the
> list that are on chr10. Here I remove the elements without 0 elements.
>
>  chr10[elementLengths(chr10) != 0]
>>
>
> Martin
>
>
>>
>> chr10<-tx_Exons[seqnames(tx_Exons)=="chr10",]
>>
>>
>>  chr10
>>>
>>
>> GRangesList of length 80922:
>>
>> $1
>>
>> GRanges with 0 ranges and 3 metadata columns:
>>
>>     seqnames    ranges strand |   exon_id   exon_name exon_rank
>>
>>        <Rle> <IRanges>  <Rle> | <integer> <character> <integer>
>>
>>
>> $2
>>
>> GRanges with 0 ranges and 3 metadata columns:
>>
>>       seqnames ranges strand | exon_id exon_name exon_rank
>>
>>
>> $3
>>
>> GRanges with 0 ranges and 3 metadata columns:
>>
>>       seqnames ranges strand | exon_id exon_name exon_rank
>>
>>
>> ...
>>
>> <80919 more elements>
>>
>> ---
>>
>> seqlengths:
>>
>>                    chr1                  chr2 ...        chrUn_gl000249
>>
>>               249250621             243199373 ...                 38502
>>
>>
>>
>>  length(chr10)
>>>
>>
>> [1] 80922
>>
>>  length(tx_Exons)
>>>
>>
>> [1] 80922
>>
>>
>> Thank you
>>
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>>
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