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  • CNV-seq output (how to know insertion or deletion)

    Hello,

    I read several postings related with CNV-seq output.
    However, I have one more additional question.

    The output of CNV-seq looks like this.

    cnv chromosome start end size log2 p.value
    CNVR_1 chrchr7 10587171 10675471 88301 1.857456 6.047393e-136
    CNVR_2 chrchr7 17103711 17174351 70641 0.8851309 6.305107e-36
    CNVR_3 chrchr7 22083831 22154471 70641 1.543111 5.88909e-86
    CNVR_4 chrchr7 23885151 23955791 70641 0.7267016 1.549861e-25

    ==================================

    In this case, can we say if the log2 value is positive, then that CNV is insertion and log2 value is negative, then CNV is deletion. Is it right?
    Then, how can I differentiate with duplication and insertion?

    Could you PLEASE help me with this?

  • #2
    I am also interested in this. Do you know how to plot for a single chromosome? I am getting this error

    plot.cnv(data,chromosome=12)
    Error in if (glim[1] == 0) glim[1] <- min(data$p.value[data$p.value > :
    missing value where TRUE/FALSE needed


    my data looks a lot like yours...

    Comment


    • #3
      For the single chromosome plotting,

      as far as I know you can use
      > plot.cnv.chr(data, chromosome=number, from = xx, to=xx)

      I hope it helps,

      Comment


      • #4
        regarding your original question about insertion and deletion. Im re-reading the paper. from page 2/9 the predicted copy number ratio is r = z * (N_Y)/(N_X). if this value is then log transformed, and the value is negative, then there is more mean copy number in N_X. if the value is positive then there is more mean copy number in N_Y.

        the paper says that N_Y is the reference,so if the above is correct, then if N_Y > N_X that implies a deletion. and N_Y < N_X this implies an insertion of copy number.

        Is there more references to double check this?

        thank you
        AC

        Comment


        • #5
          do you know what the cnv column means?
          For instance, say in R you use

          data <- read.delim("test.hits-vs-ref.hits.log2-0.6.pvalue-0.001.cnv")

          this data$cnv is all integers.... do you know the documentation to what this column means? I have looked at the manual and still don't know what the cnv column means.


          thank you again

          AC

          Comment


          • #6
            Originally posted by younko View Post
            Hello,

            I read several postings related with CNV-seq output.
            However, I have one more additional question.

            The output of CNV-seq looks like this.

            cnv chromosome start end size log2 p.value
            CNVR_1 chrchr7 10587171 10675471 88301 1.857456 6.047393e-136
            CNVR_2 chrchr7 17103711 17174351 70641 0.8851309 6.305107e-36
            CNVR_3 chrchr7 22083831 22154471 70641 1.543111 5.88909e-86
            CNVR_4 chrchr7 23885151 23955791 70641 0.7267016 1.549861e-25

            ==================================

            In this case, can we say if the log2 value is positive, then that CNV is insertion and log2 value is negative, then CNV is deletion. Is it right?
            Then, how can I differentiate with duplication and insertion?

            Could you PLEASE help me with this?
            Yes, positive log2 means more copies in "test" than "ref".

            Comment


            • #7
              Originally posted by arcolombo698 View Post
              do you know what the cnv column means?
              For instance, say in R you use

              data <- read.delim("test.hits-vs-ref.hits.log2-0.6.pvalue-0.001.cnv")

              this data$cnv is all integers.... do you know the documentation to what this column means? I have looked at the manual and still don't know what the cnv column means.


              thank you again

              AC
              The "cnv" column is the CNV region ID (0 means that window is not part of any CNV).

              Comment

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