User: Haiying.Kong

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Haiying.Kong110
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Germany
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6 days, 16 hours ago
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Posts by Haiying.Kong

<prev • 67 results • page 1 of 7 • next >
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Comment: C: Warning for "readVcfAsVRanges"
... Thank you so much for always being so helpful :) ...
written 6 days ago by Haiying.Kong110
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Warning for "readVcfAsVRanges"
... For the following line ``` vr = readVcfAsVRanges(paste0("Data/", vcf.file), "human_g1k_v37") ``` I get warning message: ``` Warning messages: 1: In .bcfHeaderAsSimpleList(header) : duplicate keys in header will be forced to unique rownames ``` Could any one please explain to me what this me ...
software error written 9 days ago by Haiying.Kong110 • updated 7 days ago by Martin Morgan ♦♦ 23k
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Installation of RCurl
... I am trying to install RCurl package on R 3.5.0. Toward end, I get the error message: ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded Error: package or namespace ...
package installation written 4 months ago by Haiying.Kong110 • updated 4 months ago by Martin Morgan ♦♦ 23k
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distGPS in chroGPS package
... On the example code:  x <- rbind(c(rep(0,15),rep(1,5)),c(rep(0,15),rep(1,5)),c(rep(0,19),1),c(rep(1,5),rep(0,15))) rownames(x) <- letters[1:4]  d <- distGPS(x,metric='tanimoto')     If I have non 0 or 1 values in the matrix, distGPS gives error message. Why do we have this restriction? ...
chrogps written 12 months ago by Haiying.Kong110 • updated 10 months ago by oscar.reina0
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Comment: C: Color specific genes in cummeRbund scatterplot
...  geom_point(aes(color=color.vector)) ...
written 19 months ago by Haiying.Kong110
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Answer: A: detecting of CNV in WGS/WES data
... I used cn.mops for WES. ...
written 20 months ago by Haiying.Kong110
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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 20 months ago by Haiying.Kong110
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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 20 months ago by Haiying.Kong110
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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 20 months ago by Haiying.Kong110
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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 20 months ago by Haiying.Kong110

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Scholar 20 months ago, created an answer that has been accepted. For A: about reshaping a data frame

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