User: Haiying.Kong

gravatar for Haiying.Kong
Haiying.Kong110
Reputation:
110
Status:
Trusted
Location:
Germany
Last seen:
2 weeks, 4 days ago
Joined:
2 years, 11 months ago
Email:
H***********@gmail.com

Posts by Haiying.Kong

<prev • 65 results • page 1 of 7 • next >
1
vote
1
answer
60
views
1
answer
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 18 days ago by Haiying.Kong110 • updated 17 days ago by Martin Morgan ♦♦ 22k
0
votes
1
answer
141
views
1
answer
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 8 months ago by Haiying.Kong110 • updated 6 months ago by oscar.reina0
0
votes
1
answers
319
views
1
answers
Comment: C: Color specific genes in cummeRbund scatterplot
...  geom_point(aes(color=color.vector)) ...
written 15 months ago by Haiying.Kong110
0
votes
1
answers
313
views
1
answers
Answer: A: detecting of CNV in WGS/WES data
... I used cn.mops for WES. ...
written 16 months ago by Haiying.Kong110
0
votes
1
answers
293
views
1
answers
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 16 months ago by Haiying.Kong110
0
votes
1
answers
713
views
1
answers
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 16 months ago by Haiying.Kong110
0
votes
0
answers
225
views
0
answers
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 16 months ago by Haiying.Kong110
0
votes
1
answers
713
views
1
answers
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 16 months ago by Haiying.Kong110
0
votes
1
answer
713
views
1
answer
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 16 months ago by Haiying.Kong110 • updated 16 months ago by Ou, Jianhong1.1k
0
votes
2
answers
310
views
2
answers
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 16 months ago by Haiying.Kong110

Latest awards to Haiying.Kong

Scholar 16 months ago, created an answer that has been accepted. For A: about reshaping a data frame

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 246 users visited in the last hour