User: Frocha

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Frocha0
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Posts by Frocha

<prev • 16 results • page 1 of 2 • next >
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Comment: C: reduce function in GenomicRanges
... Thank you very much! ...
written 4 months ago by Frocha0
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Comment: C: reduce function in GenomicRanges
... Thank you very much! However, I wish to have a function which allows min.gapwidth option. Is there a way to do so? ...
written 4 months ago by Frocha0
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Comment: C: reduce function in GenomicRanges
... Here is an example: > seqinfo <- Seqinfo("chr1", + seqlengths=100, + isCircular=TRUE) > > gr=GRanges("chr1", IRanges(c(5, 95), c(10, 101)), + strand="*",seqinfo=seqinfo) > > reduce(gr,min.gapwidth=10) GRanges object with 2 ranges and 0 metadata columns:       seqnames    ranges st ...
written 4 months ago by Frocha0
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reduce function in GenomicRanges
... How to combine genomic intervals with gap widths (e.g., <100) on a circular reference sequence? The reduce() does not work well for intervals nearby the base with coordinate 1. ...
genomicranges reduce written 4 months ago by Frocha0 • updated 4 months ago by Hervé Pagès ♦♦ 13k
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Comment: C: How to suppress the out-of-bound warnings in GenomicRanges function resize()
... Thanks for the reply! ...
written 4 months ago by Frocha0
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How to suppress the out-of-bound warnings in GenomicRanges function resize()
... Since trim() will be used after the resize(), how to suppress the "out-of-bound" warnings in GenomicRanges function resize() ? ...
genomicranges resize written 4 months ago by Frocha0 • updated 4 months ago by Hervé Pagès ♦♦ 13k
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Comment: C: How to find the end position of a read?
... One more question: what the use of N.regions.removed argument in the function GenomicAlignments::cigarWidthAlongReferenceSpace() ?     ...
written 4 months ago by Frocha0
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Answer: A: How to find the end position of a read?
... Thanks for both answers! ...
written 4 months ago by Frocha0
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How to find the end position of a read?
... I have a .sam file (for single-end reads) and I wish to find the end position of each read. I noticed that I can do that using Rsamtools if the file is a .bam file. However, I wish to do it directly on .sam file. How should I do? (using cigar value?) Thanks!   ...
alignment rsamtools cigar written 4 months ago by Frocha0
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Unknown annotation in the RGChannelSetExtended object
... I use read.metharray.exp() in the minfi package to read .IDAT files from Illumina MethylationEPIC array. I got an unknown annotation: > rgSet<-read.metharray.exp(base="IDAT/",extended=TRUE) > rgSet RGChannelSetExtended (storageMode: lockedEnvironment) assayData: 1051943 features, 8 samples ...
annotation minfi idat epic written 9 months ago by Frocha0 • updated 8 months ago by xue.zhang0

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