[R] looping in R

[Jeff Newmiller]

You desperately need to read the Posting Guide (mentioned in the footer of this email) which warns you not to post in HTML format, and learn how to make a reproducible example (e.g. http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example).

The problem lies in some interaction between your data and code, and without both we cannot help you.
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Sent from my phone. Please excuse my brevity.

On April 2, 2014 12:15:51 PM PDT, Abugri James <jabugri at uds.edu.gh> wrote:
>I ran the following loop on my SNP data and got an error message as
>indicated
>for (i in genenames){
>+   current <- fst1[which(fst1$Gene == i),]
>+   num <- nrow(current)
>+   fst <- max(current$fst)
>+   position <- mean(current$pos)
>+   nposition <- mean(current$newpos)
>+   numhigh <- nrow(current[which(current$fst > threshold),])
>+   colors <- mean(current$colors)
>+   output <- matrix(NA,nrow=1,ncol=8)
>+   numthresh <- paste("# SNPs > Fst = ", threshold, sep="")
>+   colnames(output) <- c("gene", "gene_old", "pos", "newpos", "#
>Snps",
>numthresh, "Max.Fst", "colors")
>+   output[1,1] <- i
>+   output[1,2] <- as.character(current[1, "gene_old"])
>+   output[1,3] <- position
>+   output[1,4] <- nposition
>+   output[1,5] <- num
>+   output[1,6] <- numhigh
>+   output[1,7] <- fst
>+   output[1,8] <- colors
>+   maxfstgene <- rbind(maxfstgene, output)
>+ }
>Error in output[1, 2] <- as.character(current[1, "gene_old"]) :
>  replacement has length zero
>In addition: Warning message:
>In mean.default(current$pos) :
>  argument is not numeric or logical: returning NA
>--