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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