On Dec 13, 2010, at 23:23 , Justin Fincher wrote:
> I apologize for the lack of example. I was trying not to be too long
> winded. Below is the first portion of my function that is causing the
> error. (I'm including both calls to cor(), though it quits after the first
> throws an error). I do not believe he has redefined cor() as he is a novice
> user and we tried this after starting a fresh session. And I will look into
> upgrading. I realize it is a little out of date since it is the version in
> the repository for my distribution and not the latest-and-greatest from R.
> I just didn't realize a change like that would be made that would
> (seemingly to me) reduce functionality. Thank you again for your help.
Well, let me put it this way: Once you realize what you are doing, you will
appreciate that R is not letting you do that anymore...
>
> - Fincher
>
> # As they don't change, hard code gene density values
> gene_densities =
> data.frame(chrom=c("chr1","chr2","chr3","chr4","chr5","chr6","chr7",
>
> "chr8","chr9","chr10","chr11","chr12","chr13",
>
> "chr14","chr15","chr16","chr17","chr18","chr19",
>
> "chr20","chr21","chr22","chrX","chrY"),
>
> avg_density=c(10.19,6.457,6.71,4.917,6.083,7.491,7.453,
> 5.939,7.27,7.132,11.38,9.429,3.757,
> 7.607,8.455,11.81,17.84,4.649,26.52,
> 11.19,6.51,11.28,7.535,2.931))
>
> acc_averages = c()
>
> # subset out relevant data
> accessibility_data = subset(accessibility_data,
> accessibility_data$V9==";color=000000")
>
> # calculate mean accessibility value for each chromosome
> for(i in seq(1,22)){
> sub = paste("chr",i,sep="")
> temp = subset(accessibility_data,accessibility_data$V1==sub)
> acc_averages = rbind(acc_averages,c(sub,as.double(mean(temp$V6))))
> }
> temp = subset(accessibility_data,accessibility_data$V1=="chrX")
> acc_averages = rbind(acc_averages,c("chrX",as.double(mean(temp$V6))))
This and the similar line 3 lines earlier is the culprit. The c() construct
creates a character vector because its 1st argument is character. Hence,
acc_averages is a character matrix. Now, are you _sure_ you know what happens
if you correlate something with the character vector acc_averages[,2]? It may
have given you the right thing for Pearson correlations, but it certainly did
not for rank correlations pre 2.11.0, leading to a "non-bug report" and the
subsequent check for numeric data. What happened then was that ranks were based
on the _alphabetical_ ordering of data!
I'm fairly confident that you'd really want to do the whole thing with a
suitable aggregate() call, but for now, how about just keeping the labels and
the values in two separate vectors?
--
Peter Dalgaard
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd....@cbs.dk Priv: pda...@gmail.com
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