User: Haiying.Kong

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Haiying.Kong110
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Posts by Haiying.Kong

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How to change seqlevels in a GRanges object
... I need to get rid of "chr" in seqlevels. I tried many things, including: renameSeqlevels( gr, gsub("chr", "", seqlevels(gr))) none of them worked. ...
granges written 2.5 years ago by Haiying.Kong110 • updated 2.5 years ago by Ou, Jianhong1.2k
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Answer: A: FlowCore/FlowViz: How do I skip plotting of empty populations that would otherwi
... If an empty .fcs file does not have even a header, and the file size is 0, add to between the line 1 and the line 2: idx = which( file.info(fn)$size > 0 ) fn = fn[idx]     ...
written 2.5 years ago by Haiying.Kong110
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Comment: C: Interpreting R code with GRanges object
... Yes, you are right. I gave up. Since the package does not have method for merging "CNVDetectionResult", I was trying to merge cnvr slots in the objects in consistent way as the author did. I will do it in my own way. ...
written 2.5 years ago by Haiying.Kong110
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Comment: C: reduce function after combining 2 GRanges objects from cn.mops output
... Thanks again for your help. findOverlaps() needs 2 GRanges objects, query and subject, and find overlaps between them. This is slightly different from what I am trying to do. I have only one GRanges object, and the ranges in this object has overlapping genomic regions. I am trying to collapse those ...
written 2.5 years ago by Haiying.Kong110
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Comment: C: sortSeqlevels is not sorting for GRanges object
... Thank you very much for your quick reply. sort(a) did the job. In cn.mops source code:             cnvrR <- GenomicRanges::reduce(GRanges(seqnames = segDfSubset$chr,                 IRanges(segDfSubset$start, segDfSubset$end),                 seqinfo = seqinfo(grAllRegions)))             cnvrR ...
written 2.5 years ago by Haiying.Kong110
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sortSeqlevels is not sorting for GRanges object
... Someone please help me. After applying sortSeqlevels on a GRanges object, the ranges are not sorted. > class(a) [1] "GRanges" attr(,"package") [1] "GenomicRanges" > a GRanges object with 10 ranges and 4 metadata columns:        seqnames                 ranges strand | sampleName     median   ...
granges written 2.5 years ago by Haiying.Kong110 • updated 2.5 years ago by Michael Lawrence11k
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Comment: C: reduce function after combining 2 GRanges objects from cn.mops output
... I tried, and it works now. Concatenating is working correctly now. For merging with the function "reduce",  min.gapwidth cannot do what I am trying to do: Ranges separated by a gap of at least min.gapwidth positions are not merged. Is there any way to set a restriction abou ...
written 2.5 years ago by Haiying.Kong110
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Comment: C: reduce function after combining 2 GRanges objects from cn.mops output
... > class(CNVs) [1] "CNVDetectionResult" attr(,"package") [1] "cn.mops" > cnv = cnvs(CNVs)[1:4, ] > cnv GRanges object with 4 ranges and 4 metadata columns:       seqnames               ranges strand | sampleName     median      mean          <Rle>            <IRanges>  <Rle> ...
written 2.5 years ago by Haiying.Kong110
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Comment: C: reduce function after combining 2 GRanges objects from cn.mops output
... Thank you very much for your reply. (1) I need 2 ways of combining. One is merging, one is concatenating for 2 GRanges objects with compatible elementMetadata.   For the second case, if I run cnv = c(cnv1, cnv2) on GRanges objects created by cn.mops, this gives GRangesList object. If I run  cnv = ...
written 2.5 years ago by Haiying.Kong110
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reduce function after combining 2 GRanges objects from cn.mops output
...   I have 2 GRanges objects: > cnv1 GRanges object with 3 ranges and 7 metadata columns:       seqnames             ranges strand |   T10229   T10380   T10713    T2523          <Rle>          <IRanges>  <Rle> | <factor> <factor> <factor> <factor>   [1]   ...
cn.mops granges written 2.5 years ago by Haiying.Kong110 • updated 2.5 years ago by Michael Lawrence11k

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Popular Question 13 months ago, created a question with more than 1,000 views. For How to change seqlevels in a GRanges object
Scholar 2.5 years ago, created an answer that has been accepted. For A: about reshaping a data frame

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