Re: [R] looping in R
On 02/04/2014, 3:15 PM, Abugri James wrote:
I ran the following loop on my SNP data and got an error message as
indicated
I would assume that the error message is accurate:
as.character(current[1, "gene_old"]) has length zero. You'll need to
debug why that happened.
Duncan Murdoch
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$pos) :
argument is not numeric or logical: returning NA
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Re: [R] looping in R
You desperately need to read the Posting Guide (mentioned in the footer of this
email) which warns you not to post in HTML format, and learn how to make a
reproducible example (e.g.
http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example).
The problem lies in some interaction between your data and code, and without
both we cannot help you.
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On April 2, 2014 12:15:51 PM PDT, Abugri James wrote:
>I ran the following loop on my SNP data and got an error message as
>indicated
>for (i in genenames){
>+ current <- fst1[which(fst1$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
>--
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[R] looping in R
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
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
