[Bioc-sig-seq] minoverlap error in countOverlaps

[Steve Lianoglou]

Hi Kunbin,

On Fri, Jul 22, 2011 at 2:11 AM, Kunbin Qu <KQu at genomichealth.com> wrote:
> Hi,
>
> I am trying to use "minoverlap" in the "countOverlaps" function to tune the counts between entrez genes (annEx) and my reads (a Granges object: grNons). But somehow it ran into a warning message, which unfortunately did not give me why that parameter was not used. When "minoverlap" was not used, it worked fine. Thanks.

I suspect this might be due to an outdate version of GenomicRanges?

Can you show us your sessionInfo? Did you upgrade to the latest
R/Bioconductor version as was previously suggested?

In the latest version of GenomicRanges (only available with the latest
version of bioconductor (which is only available with the latest
version of R)), you'll find that countOverlaps can take a custom
minoverlap parameter in the scenario you are using it in.

HTH,
-steve

>
> -Kunbin
>
>
> grExNons<-countOverlaps(query=annEx, subject=grNons)
> head(grExNons)
> [1] 133 1 28 58 637   0
> grExNons<-countOverlaps(query=annEx, subject=grNons, minoverlap = 5L)
> Warning message:
> In countOverlaps(query = annEx, subject = grNons, minoverlap = 5L) :
>         'minoverlap' argument is ignored
>
> hg19KG <- makeTranscriptDbFromUCSC(genome = "hg19", tablename = "knownGene")
> annEx<-exonsBy(hg19KG, "gene")
> annEx
> GRangesList of length 20545
> $1
> GRanges with 15 ranges and 2 elementMetadata values
>        seqnames               ranges strand |   exon_id   exon_name
>                <Rle>            <IRanges>  <Rle> | <integer> <character>
>        [1]    chr19 [58858174, 58858395]      - |    253677          NA
>        [2]    chr19 [58858719, 58859006]      - |    253678          NA
>  [3]    chr19 [58859832, 58860494]      - |    253688          NA
>        .....
>
>>grNons
> GRanges with 27421835 ranges and 0 elementMetadata values
>           seqnames                 ranges strand   |
>              <Rle>              <IRanges>  <Rle>   |
>       [1]    chr11 [ 48034060,  48034095]      *   |
>       [2]    chr13 [103319962, 103319997]      *   |
>       [3]     chr2 [198350561, 198350596]      *   |
>       [4]    chr12 [ 41850809,  41850844]      *   |
>       [5]    chr16 [ 89974865,  89974900]      *   |
>       [6]     chr1 [172113839, 172113874]      *   |
>       [7]    chr12 [111080272, 111080307]      *   |
>       [8]     chr2 [179445437, 179445472]      *   |
>       [9]    chr10 [119817069, 119817104]      *   |
>       ...      ...                    ...    ... ...
> [27421827]    chr17 [ 43334904,  43334939]      *   |
> [27421828]     chr6 [163903657, 163903692]      *   |
> [27421829]    chr18 [ 74737099,  74737134]      *   |
> [27421830]    chr13 [ 78311617,  78311652]      *   |
> [27421831]     chr4 [170541832, 170541867]      *   |
> [27421832]    chr13 [ 32601946,  32601981]      *   |
> [27421833]     chr3 [ 38420019,  38420054]      *   |
> [27421834]     chr8 [ 74561716,  74561751]      *   |
> [27421835]     chr3 [ 39319812,  39319847]      *   |
>
> seqlengths
>  chr1 chr10 chr11 chr12 chr13 chr14 ...  chr6  chr7  chr8  chr9  chrX  chrY
>    NA    NA    NA    NA    NA    NA ...    NA    NA    NA    NA    NA    NA
>> summary(width(grNons))
>   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.
>  18.00   36.00   36.00   35.85   36.00   36.00
>>
>
>
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-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact