Thank you all for your help. It's working now. I chose to use the sqldf
method and fn$ in the gsubfn package. I used fn$ so that I could put
variables into the sqldf statement. This helped me to increase or decrease
the window size in the Gene dataframe if I wanted to include values in the
average both before or after the gene.
For anyone else interested, this is what it looked like.
Avg_func<-function(chr,begin,finish){
fn$sqldf(paste("select d1C",chr,".'ORF', avg(C0), avg(C1)
from d1C",chr,", d2C",chr,"
where d2C",chr,".Pos between d1C",chr,".Start-",begin," and
d1C",chr,".End+",finish,"
group by d1C",chr,".'ORF'",sep=""))
}
I used d1C1 etc. because I had a different file for each chromosome that I
read into separate dataframes in R. The dataframes also had ORF (Open
Reading Frame) instead of Group.
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