User: Haiying.Kong

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Haiying.Kong90
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Germany
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1 week, 6 days ago
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1 year, 9 months ago
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Posts by Haiying.Kong

<prev • 63 results • page 1 of 7 • next >
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Comment: C: Color specific genes in cummeRbund scatterplot
...  geom_point(aes(color=color.vector)) ...
written 20 days ago by Haiying.Kong90
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Answer: A: detecting of CNV in WGS/WES data
... I used cn.mops for WES. ...
written 4 weeks ago by Haiying.Kong90
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Answer: A: about reshaping a data frame
... Because there are redundancies: 22M ATR INDEL 22M ATR SNV   and 11M BTK SNV 11M BTK INDEL you cannot do reshaping on the original data.  you need to collapse the data to something like: Sample Gene Type 22M AEBP1 SNV 17M AEBP1 SNV 22M ...
written 7 weeks ago by Haiying.Kong90
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Comment: C: How to change seqlevels in a GRanges object
... I found what the problem is. The original GRangres object is: anno.database = toGRanges(EnsDb.Hsapiens.v75, feature="gene") if I run  seqlevelsStyle(anno.database) <- "NCBI" This works. But I deleted some rows in the object to keep only Chr1:22, X, Y. If I run seqlevelsStyle after deleting ...
written 7 weeks ago by Haiying.Kong90
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Comment: C: Filter CNVs if contain certain gene
... In the same line as  James W. MacDonald. You probably can get more help if you could show us a few lines of your GRanges object. If gene names are stored as names of ranges:     idx = which(names(gr) %in% gene.list)     gr = gr[idx, ] If gene names are stored as a column in elementMetadata slot ...
written 7 weeks ago by Haiying.Kong90
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Comment: C: How to change seqlevels in a GRanges object
... I tried a second ago, and got: > anno.database GRanges object with 58153 ranges and 1 metadata column:              seqnames               ranges strand |   gene_name                 <Rle>            <IRanges>  <Rle> | <character>      DDX11L1     chr1       [11869, 14412 ...
written 7 weeks ago by Haiying.Kong90
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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 7 weeks ago by Haiying.Kong90 • updated 7 weeks ago by Ou, Jianhong990
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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 7 weeks ago by Haiying.Kong90
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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 7 weeks ago by Haiying.Kong90
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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 7 weeks ago by Haiying.Kong90

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