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 I realize it is a little out of date since it is the version in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.
- 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$V6))))
# Output the correlation without including chromosome Y
correlation = cor(acc_averages[,2],gene_densities$avg_density[1:23])
cat("Correlation w/o chrY:",correlation,'\n')
temp = subset(accessibility_data,accessibility_data$V1=="chrY")
acc_averages = rbind(acc_averages,c("chrY",mean(temp$V6)))
# Output overall correlation
correlation = cor(acc_averages[,2],gene_densities$avg_density)
cat("Correlation w/chrY:",correlation,'\n')
On Mon, Dec 13, 2010 at 17:06, Joshua Wiley <jwiley.ps...@gmail.com> wrote:
> Hi Fincher,
>
> cor() only works on numeric arguments now (as of R 2.11 or 2.10 if
> memory serves). So, I would update your function to ensure that you
> are only passing numeric data to cor() and the error should go away
> (it will probably be easier on you if you can update your version of R
> to the latest and greatest...quite a bit has changed since 2.8.1). If
> you post a reproducible example of your function, I'm sure we can help
> update it.
>
> Cheers,
>
> Josh
>
> On Mon, Dec 13, 2010 at 1:56 PM, Justin Fincher <finc...@cs.fsu.edu>
> wrote:
> > Howdy,
> > I have written a small function to generate a simple plot and my
> > colleague is having an error when attempting to run it. Essentially I
> loop
> > through categories in a data frame and take the average value for each
> > category The categories are in $V1, subset first then mean taken and
> > concatenated to previous values using rbind(c("label",mean(data$V6)).
> The
> > result is a two-column matrix with labels in column one and values in
> column
> > two. Within the function I calculate the correlation of column two and
> > another set of values that are part of the function. On my computer
> (linux
> > box running R 2.8.1) the function runs correctly. On my colleague's
> > computer (Windows box running R 2.12) the function throws an error at the
> > cor() function call saying that "x must be numeric." We are running on
> the
> > exact same data set and source'ing the same function definition. Any
> help
> > would be appreciated.
> >
> > - Fincher
> >
> > [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
>
>
> --
> Joshua Wiley
> Ph.D. Student, Health Psychology
> University of California, Los Angeles
> http://www.joshuawiley.com/
>
> --
> This message has been scanned for viruses and
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>
>
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