I'm running into difficulties reshaping a large dataframe. And I've been relatively fortunate in avoiding reshaping problems in the past, which also means I'm terrible at it.
My current dataframe looks something like this:
unique_id seq response detailed.name treatment a N1 123.23 descr. of N1 T1 a N2 231.12 descr. of N2 T1 a N3 231.23 descr. of N3 T1 ... b N1 343.23 descr. of N1 T2 b N2 281.13 descr. of N2 T2 b N3 901.23 descr. of N3 T2 ...
And I'd like:
seq detailed.name T1 T2 N1 descr. of N1 123.23 343.23 N2 descr. of N2 231.12 281.13 N3 descr. of N3 231.23 901.23
I've looked into the reshape package, but I'm not sure how I can convert the treatment factors into individual column names.
Edit: I tried running this on my local machine (4GB dual-core iMac 3.06Ghz) and it keeps failing with:
> d.tmp.2 <- cast(d.tmp, `SEQ_ID` + `GENE_INFO` ~ treatments) Aggregation requires fun.aggregate: length used as default R(5751) malloc: *** mmap(size=647168) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug
I'll try running this on one of our bigger machines when I get a chance.
reshape always seems tricky to me too, but it always seems to work with a little trial and error. Here's what I ended up finding:
> x unique_id seq response detailed.name treatment 1 a N1 123.23 dN1 T1 2 a N2 231.12 dN2 T1 3 a N3 231.23 dN3 T1 4 b N1 343.23 dN1 T2 5 b N2 281.13 dN2 T2 6 b N3 901.23 dN3 T2 > x2 <- melt(x, c("seq", "detailed.name", "treatment"), "response") > x2 seq detailed.name treatment variable value 1 N1 dN1 T1 response 123.23 2 N2 dN2 T1 response 231.12 3 N3 dN3 T1 response 231.23 4 N1 dN1 T2 response 343.23 5 N2 dN2 T2 response 281.13 6 N3 dN3 T2 response 901.23 > cast(x2, seq + detailed.name ~ treatment) seq detailed.name T1 T2 1 N1 dN1 123.23 343.23 2 N2 dN2 231.12 281.13 3 N3 dN3 231.23 901.23
Your original data was already in long format, but not in the long format that melt/cast uses. So I re-melted it. The second argument (id.vars) is list of things not to melt. The third argument (measure.vars) is the list of things that vary.
Then, the cast uses a formula. Left of the tilde are the things that stay as they are, and right of the tilde are the columns that are used to condition the value column.
More or less...!
Building on Harlan's answer - the remelting step can be avoided if the data is already in the long format, and the column holding values is specified in the
> x <- read.table(textConnection(" unique_id seq response detailed.name treatment + 1 a N1 123.23 dN1 T1 + 2 a N2 231.12 dN2 T1 + 3 a N3 231.23 dN3 T1 + 4 b N1 343.23 dN1 T2 + 5 b N2 281.13 dN2 T2 + 6 b N3 901.23 dN3 T2")) > > cast(x, seq + detailed.name ~ treatment, value = "response") seq detailed.name T1 T2 1 N1 dN1 123.23 343.23 2 N2 dN2 231.12 281.13 3 N3 dN3 231.23 901.23