cn.MOPS output - mean/median of what?
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liorglic ▴ 10
@liorglic-22928
Last seen 13 months ago

Hello, I ran the cn.mops function from the cn.MOPS package. the result summary looks something like this:

> cnvs(res)
GRanges object with 1377 ranges and 4 metadata columns:
         seqnames            ranges strand |                     sampleName            median              mean          CN
            <Rle>         <IRanges>  <Rle> |                       <factor>         <numeric>         <numeric> <character>
     [1]        1     422501-424500      * | SRR1945750_map_to_pan.sort.bam -5.32162981450578 -4.24086714482953         CN0
     [2]        1     549001-551000      * | SRR1945750_map_to_pan.sort.bam -5.30710850629932 -4.23403617330407         CN0
     [3]        1   1520501-1522500      * | SRR1945750_map_to_pan.sort.bam -2.65055434731966 -2.65575883915951         CN0
     [4]        1   2615001-2617500      * | SRR1945750_map_to_pan.sort.bam -5.32192809488736 -5.32192809488736         CN0
     [5]        1   2854501-2856000      * | SRR1945750_map_to_pan.sort.bam -5.32192730734985 -3.88128513336841         CN0

Can someone please explain the "median" and "mean" columns? What are the values in these columns? mean/median of what? How should I interpret them? I came across this old thread, but the answer there is still not clear to me.

Thanks!

cn.MOPS CNV copy number • 64 views
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