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What data type is used for input of DNAcopy

We are using DNAcopy to analyze SNP 6.0 array. What data type is used for input of DNAcopy (column Coriell.05296 and Coriell.13330)? Is it signal intensity value after normalization?

> > data(coriell)
> > coriell
>           Clone Chromosome Position Coriell.05296 Coriell.13330 1    GS1-232B23          1        0            NA      0.207470 2   
> RP11-82d16          1      468      0.008824      0.063076 3   
> RP11-62m23          1     2241     -0.000890      0.123881 4   
> RP11-60j11          1     4504      0.075875      0.154343 5  
> RP11-111O05          1     5440      0.017303     -0.043890

I checked the manual. It says the data is a vector or matrix of data from array-CGH, ROMA, or other copy number experiments. But it does not tell me what type of data.

dnacopy cna
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updated by Biostar Biostar • written by donny.dw • donny.dw

Can I suggest you checkout the reference from where that dataset came from and see if they have normalised the dataset? https://www.nature.com/articles/ng754/_S1

Let me know if you need access to the article

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written by Mark Mark

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  • Input value of DNAcopy package
    written by donny.dw • donny.dw
    ```r head(coriell) Clone Chromosome Position Coriell.05296 Coriell.13330 1 GS1-232B23 1 0 NA 0.207470 2 RP11-82d16 1 468 0.008824 0.063076 3 RP11-62m23 1 2241 -0.000890 0.123881 …