On Jul 27, 2011, at 7:02 PM, a217 wrote:
Hello,
I have an input file:
http://r.789695.n4.nabble.com/file/n3700031/testOut.txt testOut.txt
where col 1 is chromosome, column2 is start of region, column 3 is
end of
region, column 4 and 5 is base position, column 6 is total reads,
column 7
is methylation data, and column 8 is the strand.
I would like a summary output file such as:
http://r.789695.n4.nabble.com/file/n3700031/out.summary.txt
out.summary.txt
where column 1 is chromosome, column 2 is start of region, column 3
is end
of region, column 4 is total reads in general, column 5 is total
reads >=1,
column 6 is (col4/col5) or the percentage, and at the end I'd like
to list 6
more columns based on summary results from summary() function in R.
The summary() function will be used to analyze all of the
methylation data
(col7 from input) for each region (bounded by col2 and col3).
For example for chr1 100 159 summary() gives:
Min. 1st Qu. Median Mean 3rd Qu. Max.
0.0400 0.0425 0.0450 0.0450 0.0475 0.0500
which is simply the methylation data input into summary() only in
the region
of chr1 100 159.
I know how to perform all of the required functions line-by-line,
but the
hard part for me is essentially taking the input data with multiple
positions in each region and assigning all of the summary results to
one
line identified by the region.
If any of you have any suggestions I would appreciate it.
So essentially you want to drop columns 4:5 and column 8 and calculate
a proportion of counts >= 1 and get summary stats within separate
categories of start-of-region. Is that correct?
This is probably a job for aggregate or for ddply in plyr if I felt
comfortable with it, which I don't in general. Its documentation
through the help pages is s not great IMO but there are those who love
it. And I admit the melt function is a major contributor to human
happiness. Why don't you read up on aggregate which is a base
function (in the r-sense, not in the biological sense.) I will see
what I can come up with in the meantime.
--
David Winsemius, MD
West Hartford, CT
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