what is the role of the plink .map file in copy number variation analysis?
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4.0 years ago

I use the snp array data to call the copy number variants. Then, I convert CNV to plink format, namely, .cnv .map .fam. But, I was very confused about the .map file, e.g. 1 p1-723307 0 723307

1 p1-752721 0 752721

1 p1-767096 0 767096

1 p1-779322 0 779322

1 p1-779323 0 779323

1 p1-801536 0 801536


  • How it was derived from .cnv file? and what is the role of .map file?

** When I analyze the CNV burden, the results as


    TEST      GRP          AFF        UNAFF

       N      ALL        38228       855932

    RATE      ALL        2.671        2.637

    PROP      ALL            1            1

   TOTKB      ALL        545.8        521.3

   AVGKB      ALL        205.9        198.5

with the parametere meaning:

RATE: Number of segments PROP: Proportion of sample with one or more segment TOTKB: Total kb length spanned AVGKB: Average segment size

I find the AVGKB is not equal to the average size of my CNV. **

  • So, what is the meaning of segment?


Any opinion will be appreciated!

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