Copy number variation plot (R package)

Question

[lee.jingu0626]

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.

Answer 1

[QVINTVS_FABIVS_MAXIMVS]

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

[LauferVA]

very informative post for the rest of us. +2

[lee.jingu0626]

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 you

[QVINTVS_FABIVS_MAXIMVS]

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.

[18227587469]

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

[missnc]

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.

[sophiespo]

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.