Question: Copy number variation plot (R package)
2
gravatar for lee.jingu0626
3.7 years ago by
Korea, Republic Of
lee.jingu062630 wrote:

Hi.

I want to draw the plot of Copy number variation using read depth (copy number) in R package.

I can find easily the plot using frequency or log-ratio, but it is hard to find the plot using copy number.(such as figure a)

(Paper: ReadDepth: A Parallel R Package for Detecting Copy Number Alterations from Short Sequencing Reads)

Please recommend the R package about this figure.

 

plot cnv copynumber R • 5.0k views
ADD COMMENTlink modified 3.7 years ago by QVINTVS_FABIVS_MAXIMVS2.2k • written 3.7 years ago by lee.jingu062630
4
gravatar for QVINTVS_FABIVS_MAXIMVS
3.7 years ago by
USA SoCal
QVINTVS_FABIVS_MAXIMVS2.2k wrote:

I want to draw the plot of Copy number variation using read depth (copy number) in R package...I can find easily the plot using frequency or log-ratio, but it is hard to find the plot using copy number.

You can't have both. What is your data? Microarrays or sequencing?

  • Microarrays use logR Ratio and B Allele Frequency to characterize copy number variation
  • Next generation sequencing (preferably whole genome) uses read depth, discordant paired ends, chimeric mappings, and other metrics to characterize CNVs

Read depth =/= copy number unless you normalize the values correctly.

You can infer the copy number of your microarrays as follows: I'm assuming you have microarrays because you have logR Ratio data

  • Use machine learning: You need a validated call set that was determined using the same microarray platform; then you train a model saying which calls are HOM, HET, or REF (or 3 and 4 copies in DUPs, train DELs and DUPs separately)
    • If you don't have a validated set, if your samples are large enough you can use DELs on male chrX as HOM and female chrX as HET. There's some issues with this method, but it works.
  • Clustering like kMeans: You'll form clusters of HOM, HET, REF

You'll need to plot the median logR Ratio for each CNV called in an individual. I also use the median chr log R Ratio as another dimension. Consider a probe length requirement of 3 to 5 probes minimum.

If you have any questions, I'll be glad to help. CNVs are my thing

ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by QVINTVS_FABIVS_MAXIMVS2.2k

very informative post for the rest of us. +2

ADD REPLYlink written 3.7 years ago by Vincent Laufer1.0k

Thanks for your advice. Actually, I have a sequencing data...so, can you explain the usage of read depth?

I already installed read depth, but I couldn't find the usage for plotting...

 

Chromosome  StartPosition  StopPosition  MarkerCount  TotalCN  BinnedCN  MedianLog2Ratio  MedianBAF
1 754192 5665513 455 2.67 2.67 0.366006 0.34034
1 5671786 12129969 585 3.33 3.33 0.567201 0.434788
1 10874522 11745342 130 2.67 2.67 0.321936 0.46065
1 12141461 46586340 2911 2.67 2.67 0.387681 0.334732

This is my data form.(CN : copy number)

Please explain more detailed. Thank u

 

ADD REPLYlink written 3.7 years ago by lee.jingu062630

How is this sequencing data? It's array data. You don't have markers or log2 Ratios or B allele frequencies (BAF) in sequencing data.

ADD REPLYlink written 3.7 years ago by QVINTVS_FABIVS_MAXIMVS2.2k

hi ,sir.i have the microarray data like this. i want to complete the figures just like above. could you please give me some advice? thanks. ID probename schrom chrom_strat chrom_stop value 14914 RP11-2I22 chr11 103108485 103266384 0.090696449 12553 RP11-562H1 chr18 31050118 31218061 -0.497739035 11146 RP11-328P13 chr12 19270312 19498594 0.018416397 6752 RP11-91G3 chr8 91066258 91224871 0.012090134

ADD REPLYlink written 15 months ago by 182275874690

Thank you very much for the information. Would you by any chance know a package that allows you to produce plots like the ones displayed in this question? I need to produce plots similar to those from GISTIC data and can't seem to find an easy way.

ADD REPLYlink written 3.3 years ago by missnc10

You can run GISTIC on sequencing data. It isn't that hard. There is a google group (gistic-forum) where this question is asked a lot, and I wrote a detailed solution that works for me every time.

ADD REPLYlink written 2.5 years ago by sophiespo0
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