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rif-statementgeneticweighted-average

If statement for weighted averaged in R

I have a data file that is several million lines long, and contains information from many groups. Below is an abbreviated section:

MARKER      GROUP1_A1   GROUP1_A2   GROUP1_FREQ GROUP1_N    GROUP2_A1   GROUP2_A2   GROUP2_FREQ GROUP2_N
rs10    A   C   0.055   1232    A   C   0.055   3221
rs1000  A   G   0.208   1232    A   G   0.208   3221
rs10000 G   C   0.134   1232    C   G   0.8624  3221
rs10001 C   A   0.229   1232    A   C   0.775   3221

I would like to created a weighted average of the frequency (FREQ) variable (which in itself is straightforward), however in this case some of the rows are mismatched (rows 3 & 4). If the letters do not line up, then the frequency of the second group needs to be subtracted by 1 before the weighted mean of that marker is calculated.

I would like to set up a simple IF statement, but I am unsure of the syntax of such a task.

Any insight or direction is appreciated!

Solution

  • Say you've read your data in a data frame called mydata. Then do the following:

    mydata$GROUP2_FREQ <- mydata$GROUP2_FREQ - (mydata$GROUP1_A1 != mydata$GROUP2_A1)

    It works because R treats TRUE values as 1 and FALSE values as 0.

    EDIT: Try the following instead:

    mydata$GROUP2_FREQ <- abs( (as.character(mydata$GROUP1_A1) != 
                            as.character(mydata$GROUP2_A1)) -                   
                          as.numeric(mydata$GROUP2_FREQ) )