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.

-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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